# R1107.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Fri Aug 25 11:28:10 2023 File name: R1107.pdb no. of DNA/RNA chains: 1 [0=69] no. of nucleotides: 69 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 25 base pair(s) 1 0.G1 0.U36 [G-U] 00-n/a cWW cW-W 162.6(...) C3'-endo lambda=30.1; -158.4(anti) C3'-endo lambda=70.4 d(C1'-C1')=10.10 d(N1-N9)=8.35 d(C6-C8)=9.03 tor(N1-C1'-C1'-N9)=10.9 H-bonds[2]: "O6(carbonyl)-N3(imino)[2.52]; N1(imino)-O2(carbonyl)[2.70]" bp_pars: [-2.94 -1.51 -1.55 -11.32 -3.80 -7.47] 2 0.G1 0.G60 [G+G] 00-n/a cHS cM+m 162.6(...) C3'-endo lambda=42.5; -155.6(anti) C3'-endo lambda=124.6 d(C1'-C1')=8.06 d(N1-N9)=7.81 d(C6-C8)=7.87 tor(N1-C1'-C1'-N9)=-3.9 H-bonds[2]: "N7-O2'(hydroxyl)[3.99]; O6(carbonyl)-N2(amino)[2.61]" bp_pars: [-6.30 -0.50 1.54 9.83 3.14 13.91] 3 0.G2 0.C35 [G-C] WC 19-XIX cWW cW-W 179.2(anti) C3'-endo lambda=66.9; -156.7(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.27 d(N1-N9)=8.88 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=2.4 H-bonds[3]: "N1(imino)-N3[3.11]; N2(amino)-O2(carbonyl)[2.59]; N2(amino)-N3[2.70]" bp_pars: [0.91 0.18 -0.68 -22.35 -5.05 11.85] 4 0.G3 0.C34 [G-C] WC 19-XIX cWW cW-W -172.9(anti) C3'-endo lambda=65.7; -151.9(anti) C3'-endo lambda=55.9 d(C1'-C1')=10.26 d(N1-N9)=8.82 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=0.7 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.31]; N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[2.54]; N2(amino)-N3[2.74]" bp_pars: [0.80 0.06 -0.58 -21.18 -7.32 9.86] 5 0.G4 0.C33 [G-C] WC 19-XIX cWW cW-W -175.9(anti) C3'-endo lambda=61.4; -163.1(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.49 d(N1-N9)=8.94 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=-2.4 H-bonds[4]: "O6(carbonyl)-N4(amino)[3.25]; N1(imino)-N3[2.96]; N2(amino)-O2(carbonyl)[2.53]; N2(amino)-N3[2.99]" bp_pars: [0.50 0.04 0.13 -7.39 -2.74 7.63] 6 0.G5 0.C32 [G-C] WC 19-XIX cWW cW-W -167.4(anti) C3'-endo lambda=61.7; 175.0(anti) C3'-endo lambda=38.0 d(C1'-C1')=11.32 d(N1-N9)=9.46 d(C6-C8)=10.25 tor(N1-C1'-C1'-N9)=-0.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.24]; N1(imino)*N4(amino)[2.88]; N2(amino)-N3[2.91]" bp_pars: [1.75 0.13 -0.19 -12.00 -5.95 -5.52] 7 0.C6 0.G31 [C-G] WC 19-XIX cWW cW-W -175.7(anti) C3'-endo lambda=47.7; -177.2(anti) C3'-endo lambda=53.3 d(C1'-C1')=10.74 d(N1-N9)=8.86 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-8.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.66]; N3-N1(imino)[2.72]; N4(amino)-O6(carbonyl)[2.65]" bp_pars: [-0.27 -0.30 0.09 1.93 -8.72 -2.54] 8 0.A8 0.A30 [A-A] 00-n/a cS. cm-. -156.9(anti) C3'-endo lambda=121.5; 175.9(anti) C2'-exo lambda=34.7 d(C1'-C1')=10.08 d(N1-N9)=9.64 d(C6-C8)=10.97 tor(N1-C1'-C1'-N9)=0.2 H-bonds[2]: "O2'(hydroxyl)-N1[3.44]; N3-N6(amino)[3.52]" bp_pars: [6.78 -0.32 -0.40 -10.40 -2.69 48.04] 9 0.A10 0.U69 [A-U] WC 20-XX cWW cW-W -171.9(anti) C3'-endo lambda=51.0; -157.1(anti) C3'-endo lambda=38.7 d(C1'-C1')=11.49 d(N1-N9)=9.41 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-11.2 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.49]; N1-N3(imino)[3.17]" bp_pars: [1.22 0.01 -0.55 0.24 -21.12 -17.93] 10 0.G11 0.C68 [G-C] WC 19-XIX cWW cW-W -159.3(anti) C3'-endo lambda=54.6; -160.6(anti) C3'-endo lambda=50.7 d(C1'-C1')=10.38 d(N1-N9)=8.60 d(C6-C8)=9.48 tor(N1-C1'-C1'-N9)=-10.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.47]; N1(imino)-N3[2.47]; N2(amino)-O2(carbonyl)[2.44]" bp_pars: [0.15 -0.54 0.20 -2.90 -14.69 -2.06] 11 0.C12 0.G67 [C-G] WC 19-XIX cWW cW-W -155.8(anti) C3'-endo lambda=54.3; -167.1(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.60 d(N1-N9)=8.89 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=-8.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.70]; N3-N1(imino)[2.82]; N4(amino)-O6(carbonyl)[2.87]" bp_pars: [0.01 -0.18 0.09 8.40 -11.67 0.11] 12 0.A13 0.U66 [A-U] WC 20-XX cWW cW-W -169.5(anti) C3'-endo lambda=51.5; -171.1(anti) C3'-endo lambda=57.5 d(C1'-C1')=10.66 d(N1-N9)=8.95 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=-8.4 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.11]; N1-N3(imino)[3.04]" bp_pars: [-0.65 -0.10 0.48 6.18 -9.20 -1.36] 13 0.G14 0.C65 [G-C] WC 19-XIX cWW cW-W -175.3(anti) C3'-endo lambda=48.1; -167.2(anti) C3'-endo lambda=44.0 d(C1'-C1')=11.69 d(N1-N9)=9.64 d(C6-C8)=10.19 tor(N1-C1'-C1'-N9)=-7.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.78]; N1(imino)-N3[3.41]; N2(amino)-O2(carbonyl)[3.99]" bp_pars: [0.31 0.30 -0.46 -12.43 -18.64 -15.78] 14 0.A15 0.U64 [A-U] WC 20-XX cWW cW-W -167.4(anti) C3'-endo lambda=56.4; -164.3(anti) C3'-endo lambda=55.8 d(C1'-C1')=10.49 d(N1-N9)=8.85 d(C6-C8)=9.90 tor(N1-C1'-C1'-N9)=-15.6 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.33]; N1-N3(imino)[2.90]" bp_pars: [0.03 -0.06 0.68 -1.75 -17.29 3.93] 15 0.A16 0.U63 [A-U] WC 20-XX cWW cW-W -169.8(anti) C3'-endo lambda=55.2; -114.5(anti) C2'-endo lambda=54.0 d(C1'-C1')=10.74 d(N1-N9)=9.04 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=-5.8 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.95]; N1-N3(imino)[2.95]" bp_pars: [0.35 -0.01 0.38 3.82 -5.22 -2.69] 16 0.G17 0.C29 [G-C] WC 19-XIX cWW cW-W -173.7(anti) C3'-endo lambda=51.4; -157.2(anti) C3'-endo lambda=48.4 d(C1'-C1')=11.06 d(N1-N9)=9.16 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-9.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.72]; N1(imino)-N3[3.00]; N2(amino)-O2(carbonyl)[3.18]" bp_pars: [0.09 -0.09 0.32 -3.68 -9.11 -8.45] 17 0.C18 0.G28 [C-G] WC 19-XIX cWW cW-W -174.3(anti) C3'-endo lambda=52.2; -170.4(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.79 d(N1-N9)=9.05 d(C6-C8)=10.06 tor(N1-C1'-C1'-N9)=-18.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.76]; N3-N1(imino)[2.99]; N4(amino)-O6(carbonyl)[3.28]" bp_pars: [-0.14 0.04 0.41 -1.95 -21.37 3.93] 18 0.G19 0.C27 [G-C] WC 19-XIX cWW cW-W -164.9(anti) C3'-endo lambda=54.5; -167.7(anti) C3'-endo lambda=45.7 d(C1'-C1')=10.89 d(N1-N9)=9.00 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=-16.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.81]; N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[3.04]" bp_pars: [0.45 -0.10 0.30 -22.60 -21.81 -8.11] 19 0.G28 0.A62 [G+A] Linker 00-n/a tSS tm+m -170.4(anti) C3'-endo lambda=85.8; -114.5(anti) C3'-endo lambda=60.0 d(C1'-C1')=8.29 d(N1-N9)=7.91 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=155.8 H-bonds[2]: "O2'(hydroxyl)-N1[2.78]; N2(amino)-N3[3.27]" bp_pars: [-2.66 -7.56 1.26 -38.49 -13.11 -151.25] 20 0.U38 0.C59 [U-C] 00-n/a ... c... -170.7(anti) C3'-endo lambda=9.5; -164.7(anti) C3'-endo lambda=44.9 d(C1'-C1')=11.45 d(N1-N9)=8.98 d(C6-C8)=8.74 tor(N1-C1'-C1'-N9)=32.6 H-bonds[1]: "O4(carbonyl)*N3[2.84]" bp_pars: [-3.60 -0.93 -0.86 20.36 -24.49 -56.07] 21 0.C39 0.G58 [C-G] WC 19-XIX cWW cW-W -162.6(anti) C3'-endo lambda=48.9; -163.8(anti) C3'-endo lambda=63.7 d(C1'-C1')=10.87 d(N1-N9)=9.24 d(C6-C8)=10.28 tor(N1-C1'-C1'-N9)=-7.3 H-bonds[4]: "O2(carbonyl)-N2(amino)[3.05]; N3-N1(imino)[3.36]; N3-N2(amino)[2.68]; N4(amino)*N1(imino)[3.08]" bp_pars: [-1.46 0.19 0.15 9.70 -10.81 5.25] 22 0.A40 0.U57 [A-U] WC 20-XX cWW cW-W -167.7(anti) C3'-endo lambda=55.4; -165.9(anti) C3'-endo lambda=57.0 d(C1'-C1')=10.44 d(N1-N9)=8.79 d(C6-C8)=9.78 tor(N1-C1'-C1'-N9)=-6.3 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.96]; N1-N3(imino)[2.80]" bp_pars: [-0.09 -0.16 -0.16 2.62 -12.83 2.32] 23 0.G41 0.C56 [G-C] WC 19-XIX cWW cW-W -175.9(anti) C3'-endo lambda=52.0; -165.3(anti) C3'-endo lambda=57.2 d(C1'-C1')=10.41 d(N1-N9)=8.70 d(C6-C8)=9.64 tor(N1-C1'-C1'-N9)=-5.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.81]; N1(imino)-N3[2.76]; N2(amino)-O2(carbonyl)[2.61]" bp_pars: [-0.65 -0.38 0.07 -6.97 -7.98 0.60] 24 0.C42 0.G55 [C-G] WC 19-XIX cWW cW-W 178.4(anti) C3'-endo lambda=42.7; -174.4(anti) C3'-endo lambda=51.8 d(C1'-C1')=11.35 d(N1-N9)=9.35 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-2.2 H-bonds[4]: "O2(carbonyl)-N2(amino)[3.23]; N3-N1(imino)[3.16]; N3-N2(amino)[3.35]; N4(amino)-O6(carbonyl)[2.92]" bp_pars: [-0.76 0.09 -0.12 7.62 -4.95 -6.84] 25 0.C43 0.G54 [C-G] WC 19-XIX cWW cW-W -159.2(anti) C3'-endo lambda=63.8; -167.3(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.45 d(N1-N9)=8.95 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-3.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.67]; N3-N1(imino)[3.13]; N4(amino)-O6(carbonyl)[3.53]" bp_pars: [0.78 0.09 -0.30 -1.50 -9.27 10.86] **************************************************************************** List of 2 multiplet(s) 1 nts=3* 0.G1+0.U36+0.G60 [GUG] 2 nts=3 0.C18+0.G28+0.A62 [CGA] **************************************************************************** List of 3 helices helix=1[1] bps=7 1 0.G1 0.U36 [G-U] 00-n/a cWW cW-W 2 0.G2 0.C35 [G-C] WC 19-XIX cWW cW-W 3 0.G3 0.C34 [G-C] WC 19-XIX cWW cW-W 4 0.G4 0.C33 [G-C] WC 19-XIX cWW cW-W 5 0.G5 0.C32 [G-C] WC 19-XIX cWW cW-W 6 0.C6 0.G31 [C-G] WC 19-XIX cWW cW-W 7 0.A8 0.A30 [A-A] 00-n/a cS. cm-. helix=2[2] bps=10 1 0.A10 0.U69 [A-U] WC 20-XX cWW cW-W 2 0.G11 0.C68 [G-C] WC 19-XIX cWW cW-W 3 0.C12 0.G67 [C-G] WC 19-XIX cWW cW-W 4 0.A13 0.U66 [A-U] WC 20-XX cWW cW-W 5 0.G14 0.C65 [G-C] WC 19-XIX cWW cW-W 6 0.A15 0.U64 [A-U] WC 20-XX cWW cW-W 7 0.A16 0.U63 [A-U] WC 20-XX cWW cW-W 8 0.G17 0.C29 [G-C] WC 19-XIX cWW cW-W 9 0.C18 0.G28 [C-G] WC 19-XIX cWW cW-W 10 0.G19 0.C27 [G-C] WC 19-XIX cWW cW-W helix=3[1] bps=6 1 0.U38 0.C59 [U-C] 00-n/a ... c... 2 0.C39 0.G58 [C-G] WC 19-XIX cWW cW-W 3 0.A40 0.U57 [A-U] WC 20-XX cWW cW-W 4 0.G41 0.C56 [G-C] WC 19-XIX cWW cW-W 5 0.C42 0.G55 [C-G] WC 19-XIX cWW cW-W 6 0.C43 0.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 4 stems stem=1[#1] bps=5 1 0.G2 0.C35 [G-C] WC 19-XIX cWW cW-W 2 0.G3 0.C34 [G-C] WC 19-XIX cWW cW-W 3 0.G4 0.C33 [G-C] WC 19-XIX cWW cW-W 4 0.G5 0.C32 [G-C] WC 19-XIX cWW cW-W 5 0.C6 0.G31 [C-G] WC 19-XIX cWW cW-W stem=2[#2] bps=7 1 0.A10 0.U69 [A-U] WC 20-XX cWW cW-W 2 0.G11 0.C68 [G-C] WC 19-XIX cWW cW-W 3 0.C12 0.G67 [C-G] WC 19-XIX cWW cW-W 4 0.A13 0.U66 [A-U] WC 20-XX cWW cW-W 5 0.G14 0.C65 [G-C] WC 19-XIX cWW cW-W 6 0.A15 0.U64 [A-U] WC 20-XX cWW cW-W 7 0.A16 0.U63 [A-U] WC 20-XX cWW cW-W stem=3[#2] bps=3 1 0.G17 0.C29 [G-C] WC 19-XIX cWW cW-W 2 0.C18 0.G28 [C-G] WC 19-XIX cWW cW-W 3 0.G19 0.C27 [G-C] WC 19-XIX cWW cW-W stem=4[#3] bps=5 1 0.C39 0.G58 [C-G] WC 19-XIX cWW cW-W 2 0.A40 0.U57 [A-U] WC 20-XX cWW cW-W 3 0.G41 0.C56 [G-C] WC 19-XIX cWW cW-W 4 0.C42 0.G55 [C-G] WC 19-XIX cWW cW-W 5 0.C43 0.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#2 contains 2 stems: [#2, #3] **************************************************************************** List of 2 hairpin loop(s) 1 nts=7 UUCACGU closed by pair {0.G19+0.C27 [GC], #3} 0.G19+0.U20+0.U21+0.C22+0.A23+0.C24+0.G25+0.U26+0.C27 [GUUCACGUC] 2 nts=10 AUUGCACUCC closed by pair {0.C43+0.G54 [CG], #4} 0.C43+0.A44+0.U45+0.U46+0.G47+0.C48+0.A49+0.C50+0.U51+0.C52+0.C53+0.G54 [CAUUGCACUCCG] This structure contains pseudo-knot(s). **************************************************************************** List of 1 A-minor motif(s) 1 type=I A/C-G 0.A62 vs 0.C18+0.G28 [WC] -0.C18 H-bonds[2]: "O2'(hydroxyl)-O2'(hydroxyl)[2.86]; O2'(hydroxyl)-O2(carbonyl)[2.98]" +0.G28 H-bonds[2]: "N1-O2'(hydroxyl)[2.78]; N3-N2(amino)[3.27]" **************************************************************************** >chain-0 #1 RNA with 69 nts GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU .(((((...[[[[[[[(((.......))).)))))...(((((..........)))))....]]]]]]] # r1107_df.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Fri Aug 25 11:28:10 2023 File name: r1107_df.pdb no. of DNA/RNA chains: 1 [ =69] no. of nucleotides: 69 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 24 base pair(s) 1 _.G1 _.U36 [G-U] 00-n/a cWW cW-W -174.7(anti) C3'-endo lambda=51.4; -168.3(anti) C3'-endo lambda=60.6 d(C1'-C1')=10.39 d(N1-N9)=8.73 d(C6-C8)=9.66 tor(N1-C1'-C1'-N9)=-8.7 H-bonds[4]: "O6(carbonyl)-N3(imino)[3.00]; O6(carbonyl)*O4(carbonyl)[2.99]; N1(imino)-O2(carbonyl)[2.94]; N2(amino)-O2(carbonyl)[2.72]" bp_pars: [-0.98 -0.39 -0.16 -0.54 -12.88 2.04] 2 _.G2 _.C35 [G-C] WC 19-XIX cWW cW-W -169.5(anti) C3'-endo lambda=50.3; -170.9(anti) C3'-endo lambda=49.5 d(C1'-C1')=11.11 d(N1-N9)=9.19 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-4.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.70]; N1(imino)-N3[3.02]; N2(amino)-O2(carbonyl)[3.38]" bp_pars: [-0.28 -0.13 0.06 -0.27 -9.01 -10.68] 3 _.G3 _.C34 [G-C] WC 19-XIX cWW cW-W -163.5(anti) C3'-endo lambda=54.0; -176.3(anti) C2'-exo lambda=50.7 d(C1'-C1')=11.26 d(N1-N9)=9.42 d(C6-C8)=10.21 tor(N1-C1'-C1'-N9)=-14.0 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.94]; N1(imino)-N3[3.19]; N2(amino)-O2(carbonyl)[3.28]" bp_pars: [0.11 0.19 0.02 -3.38 -14.20 -3.90] 4 _.G4 _.C33 [G-C] WC 19-XIX cWW cW-W -166.7(anti) C3'-endo lambda=54.7; -164.5(anti) C3'-endo lambda=58.1 d(C1'-C1')=10.55 d(N1-N9)=8.91 d(C6-C8)=9.85 tor(N1-C1'-C1'-N9)=-1.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.86]; N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.74]" bp_pars: [-0.47 -0.17 0.07 -1.61 -0.59 2.01] 5 _.G5 _.C32 [G-C] WC 19-XIX cWW cW-W -156.0(anti) C3'-endo lambda=56.0; -164.6(anti) C3'-endo lambda=55.5 d(C1'-C1')=10.81 d(N1-N9)=9.13 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-1.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.00]; N1(imino)-N3[3.02]; N2(amino)-O2(carbonyl)[2.78]" bp_pars: [0.03 0.07 -0.24 1.19 -7.69 3.82] 6 _.C6 _.G31 [C-G] WC 19-XIX cWW cW-W -176.1(anti) C2'-exo lambda=53.8; -159.5(anti) C3'-endo lambda=55.2 d(C1'-C1')=11.01 d(N1-N9)=9.28 d(C6-C8)=10.20 tor(N1-C1'-C1'-N9)=-11.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.87]; N3-N1(imino)[3.15]; N4(amino)-O6(carbonyl)[3.27]" bp_pars: [0.04 0.21 -0.07 -0.13 -9.36 3.57] 7 _.C7 _.A30 [C-A] 00-n/a cWW cW-W -153.1(anti) C3'-endo lambda=50.7; -140.2(anti) C1'-endo lambda=71.3 d(C1'-C1')=10.26 d(N1-N9)=8.85 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=-15.3 H-bonds[1]: "N4(amino)-N1[2.78]" bp_pars: [-1.37 -0.05 0.07 -3.02 -27.17 9.52] 8 _.A10 _.RU3/69 [A-u] WC 20-XX cWW cW-W -168.4(anti) C3'-endo lambda=55.8; -114.9(anti) C3'-exo lambda=55.9 d(C1'-C1')=10.83 d(N1-N9)=9.17 d(C6-C8)=10.09 tor(N1-C1'-C1'-N9)=9.5 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.29]; N1-N3(imino)[3.12]" bp_pars: [0.08 0.21 -0.66 -14.27 -15.51 2.24] 9 _.G11 _.C68 [G-C] WC 19-XIX cWW cW-W -169.3(anti) C3'-endo lambda=62.3; -163.9(anti) C3'-endo lambda=54.0 d(C1'-C1')=10.98 d(N1-N9)=9.42 d(C6-C8)=10.50 tor(N1-C1'-C1'-N9)=-10.1 H-bonds[3]: "N1(imino)-N3[3.40]; N2(amino)-O2(carbonyl)[2.88]; N2(amino)-N3[3.34]" bp_pars: [0.58 0.49 0.28 -3.03 -12.84 8.72] 10 _.C12 _.G67 [C-G] WC 19-XIX cWW cW-W -162.3(anti) C3'-endo lambda=63.0; -167.3(anti) C3'-endo lambda=57.6 d(C1'-C1')=10.89 d(N1-N9)=9.41 d(C6-C8)=10.57 tor(N1-C1'-C1'-N9)=-5.5 H-bonds[2]: "O2(carbonyl)-N2(amino)[2.83]; N3-N1(imino)[3.52]" bp_pars: [0.59 0.62 0.04 -1.45 -6.19 13.44] 11 _.A13 _.U66 [A-U] WC 20-XX cWW cW-W -159.7(anti) C3'-endo lambda=58.2; -155.2(anti) C3'-endo lambda=54.7 d(C1'-C1')=10.85 d(N1-N9)=9.20 d(C6-C8)=10.20 tor(N1-C1'-C1'-N9)=-7.8 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.38]; N1-N3(imino)[3.09]" bp_pars: [0.27 0.24 -0.03 -3.04 -13.22 4.19] 12 _.G14 _.C65 [G-C] WC 19-XIX cWW cW-W -158.7(anti) C3'-endo lambda=53.8; -156.3(anti) C3'-endo lambda=57.1 d(C1'-C1')=10.59 d(N1-N9)=8.91 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-14.6 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.81]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.73]" bp_pars: [-0.31 -0.18 0.07 -3.41 -11.27 0.81] 13 _.A15 _.U64 [A-U] WC 20-XX cWW cW-W -154.8(anti) C3'-endo lambda=59.3; -153.0(anti) C3'-endo lambda=60.3 d(C1'-C1')=10.28 d(N1-N9)=8.79 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-2.8 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.30]; N1-N3(imino)[2.88]" bp_pars: [-0.08 0.02 -0.29 1.71 -9.44 10.47] 14 _.A16 _.U63 [A-U] WC 20-XX cWW cW-W -166.8(anti) C3'-endo lambda=64.3; -153.9(anti) C3'-endo lambda=62.4 d(C1'-C1')=10.48 d(N1-N9)=9.15 d(C6-C8)=10.40 tor(N1-C1'-C1'-N9)=-6.3 H-bonds[1]: "N1-N3(imino)[3.30]" bp_pars: [0.35 0.56 0.10 7.10 -14.56 16.27] 15 _.G17 _.C29 [G-C] WC 19-XIX cWW cW-W -170.8(anti) C3'-endo lambda=51.2; -164.7(anti) C4'-exo lambda=55.3 d(C1'-C1')=10.66 d(N1-N9)=8.89 d(C6-C8)=9.75 tor(N1-C1'-C1'-N9)=-10.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.77]; N1(imino)-N3[2.87]; N2(amino)-O2(carbonyl)[2.78]" bp_pars: [-0.45 -0.23 -0.22 -9.53 -16.96 -0.86] 16 _.C18 _.G28 [C-G] WC 19-XIX cWW cW-W -159.1(anti) C3'-endo lambda=53.6; -165.8(anti) C3'-endo lambda=48.6 d(C1'-C1')=11.38 d(N1-N9)=9.52 d(C6-C8)=10.33 tor(N1-C1'-C1'-N9)=-14.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.50]; N3-N1(imino)[3.38]; N4(amino)-O6(carbonyl)[3.35]" bp_pars: [0.39 0.31 -0.02 -2.72 -22.54 -1.89] 17 _.C18 _.A62 [C-A] 00-n/a ... t... -159.1(anti) C3'-endo lambda=125.6; -164.2(anti) O4'-exo lambda=16.7 d(C1'-C1')=6.48 d(N1-N9)=6.13 d(C6-C8)=6.18 tor(N1-C1'-C1'-N9)=-144.6 H-bonds[1]: "O4'-N6(amino)[2.73]" bp_pars: [6.03 -8.57 1.06 20.04 1.98 5.34] 18 _.G19 _.C27 [G-C] WC 19-XIX cWW cW-W -151.7(anti) C3'-endo lambda=53.3; -161.3(anti) C3'-endo lambda=48.4 d(C1'-C1')=12.04 d(N1-N9)=10.17 d(C6-C8)=10.87 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[2]: "O6(carbonyl)-N4(amino)[3.55]; N1(imino)-N3[3.97]" bp_pars: [0.38 0.88 0.37 -5.41 -4.92 -9.08] 19 _.U20 _.A61 [U+A] 00-n/a cWH cW+M -58.8(anti) C1'-endo lambda=68.4; 166.1(anti) O4'-exo lambda=61.8 d(C1'-C1')=7.95 d(N1-N9)=6.73 d(C6-C8)=6.25 tor(N1-C1'-C1'-N9)=29.7 H-bonds[1]: "N3(imino)-N7[3.17]" bp_pars: [-0.25 3.53 -2.09 12.48 7.41 -63.15] 20 _.C39 _.G58 [C-G] WC 19-XIX cWW cW-W -163.5(anti) C3'-endo lambda=57.0; -162.7(anti) C3'-endo lambda=58.9 d(C1'-C1')=10.65 d(N1-N9)=9.07 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-11.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.72]; N3-N1(imino)[3.02]; N4(amino)-O6(carbonyl)[3.29]" bp_pars: [-0.06 0.09 0.55 -0.07 -9.69 5.73] 21 _.A40 _.U57 [A-U] WC 20-XX cWW cW-W -163.9(anti) C3'-endo lambda=57.2; -160.4(anti) C3'-endo lambda=56.2 d(C1'-C1')=11.09 d(N1-N9)=9.46 d(C6-C8)=10.48 tor(N1-C1'-C1'-N9)=-12.3 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.72]; N1-N3(imino)[3.38]" bp_pars: [0.12 0.52 0.24 -1.64 -15.11 4.83] 22 _.G41 _.C56 [G-C] WC 19-XIX cWW cW-W -164.1(anti) C3'-endo lambda=55.0; -169.0(anti) C3'-endo lambda=55.7 d(C1'-C1')=10.96 d(N1-N9)=9.27 d(C6-C8)=10.24 tor(N1-C1'-C1'-N9)=-11.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.40]; N1(imino)-N3[3.19]; N2(amino)-O2(carbonyl)[2.86]" bp_pars: [-0.26 0.23 0.27 -1.34 -11.19 4.50] 23 _.C42 _.G55 [C-G] WC 19-XIX cWW cW-W -163.4(anti) C3'-endo lambda=54.5; -173.0(anti) C2'-exo lambda=54.4 d(C1'-C1')=10.84 d(N1-N9)=9.10 d(C6-C8)=10.02 tor(N1-C1'-C1'-N9)=-13.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.80]; N3-N1(imino)[2.97]; N4(amino)-O6(carbonyl)[2.92]" bp_pars: [0.05 0.00 0.02 0.09 -14.52 2.00] 24 _.C43 _.G54 [C-G] WC 19-XIX cWW cW-W -161.5(anti) C3'-endo lambda=51.2; -167.2(anti) C3'-endo lambda=51.8 d(C1'-C1')=11.08 d(N1-N9)=9.22 d(C6-C8)=10.03 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.92]; N3-N1(imino)[3.02]; N4(amino)-O6(carbonyl)[2.85]" bp_pars: [0.02 0.01 -0.01 -0.58 -8.73 -2.40] **************************************************************************** List of 1 multiplet(s) 1 nts=3 _.C18+_.G28+_.A62 [CGA] **************************************************************************** List of 3 helices helix=1[1] bps=7 1 _.G1 _.U36 [G-U] 00-n/a cWW cW-W 2 _.G2 _.C35 [G-C] WC 19-XIX cWW cW-W 3 _.G3 _.C34 [G-C] WC 19-XIX cWW cW-W 4 _.G4 _.C33 [G-C] WC 19-XIX cWW cW-W 5 _.G5 _.C32 [G-C] WC 19-XIX cWW cW-W 6 _.C6 _.G31 [C-G] WC 19-XIX cWW cW-W 7 _.C7 _.A30 [C-A] 00-n/a cWW cW-W helix=2[2] bps=10 1 _.A10 _.RU3/69 [A-u] WC 20-XX cWW cW-W 2 _.G11 _.C68 [G-C] WC 19-XIX cWW cW-W 3 _.C12 _.G67 [C-G] WC 19-XIX cWW cW-W 4 _.A13 _.U66 [A-U] WC 20-XX cWW cW-W 5 _.G14 _.C65 [G-C] WC 19-XIX cWW cW-W 6 _.A15 _.U64 [A-U] WC 20-XX cWW cW-W 7 _.A16 _.U63 [A-U] WC 20-XX cWW cW-W 8 _.G17 _.C29 [G-C] WC 19-XIX cWW cW-W 9 _.C18 _.G28 [C-G] WC 19-XIX cWW cW-W 10 _.G19 _.C27 [G-C] WC 19-XIX cWW cW-W helix=3[1] bps=5 1 _.C39 _.G58 [C-G] WC 19-XIX cWW cW-W 2 _.A40 _.U57 [A-U] WC 20-XX cWW cW-W 3 _.G41 _.C56 [G-C] WC 19-XIX cWW cW-W 4 _.C42 _.G55 [C-G] WC 19-XIX cWW cW-W 5 _.C43 _.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 4 stems stem=1[#1] bps=5 1 _.G2 _.C35 [G-C] WC 19-XIX cWW cW-W 2 _.G3 _.C34 [G-C] WC 19-XIX cWW cW-W 3 _.G4 _.C33 [G-C] WC 19-XIX cWW cW-W 4 _.G5 _.C32 [G-C] WC 19-XIX cWW cW-W 5 _.C6 _.G31 [C-G] WC 19-XIX cWW cW-W stem=2[#2] bps=7 1 _.A10 _.RU3/69 [A-u] WC 20-XX cWW cW-W 2 _.G11 _.C68 [G-C] WC 19-XIX cWW cW-W 3 _.C12 _.G67 [C-G] WC 19-XIX cWW cW-W 4 _.A13 _.U66 [A-U] WC 20-XX cWW cW-W 5 _.G14 _.C65 [G-C] WC 19-XIX cWW cW-W 6 _.A15 _.U64 [A-U] WC 20-XX cWW cW-W 7 _.A16 _.U63 [A-U] WC 20-XX cWW cW-W stem=3[#2] bps=3 1 _.G17 _.C29 [G-C] WC 19-XIX cWW cW-W 2 _.C18 _.G28 [C-G] WC 19-XIX cWW cW-W 3 _.G19 _.C27 [G-C] WC 19-XIX cWW cW-W stem=4[#3] bps=5 1 _.C39 _.G58 [C-G] WC 19-XIX cWW cW-W 2 _.A40 _.U57 [A-U] WC 20-XX cWW cW-W 3 _.G41 _.C56 [G-C] WC 19-XIX cWW cW-W 4 _.C42 _.G55 [C-G] WC 19-XIX cWW cW-W 5 _.C43 _.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#2 contains 2 stems: [#2, #3] **************************************************************************** List of 2 hairpin loop(s) 1 nts=7 UUCACGU closed by pair {_.G19+_.C27 [GC], #3} _.G19+_.U20+_.U21+_.C22+_.A23+_.C24+_.G25+_.U26+_.C27 [GUUCACGUC] 2 nts=10 AUUGCACUCC closed by pair {_.C43+_.G54 [CG], #4} _.C43+_.A44+_.U45+_.U46+_.G47+_.C48+_.A49+_.C50+_.U51+_.C52+_.C53+_.G54 [CAUUGCACUCCG] This structure contains pseudo-knot(s). **************************************************************************** >chain-_ #1 RNA with 69 nts GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCu .(((((...[[[[[[[(((.......))).)))))...(((((..........)))))....]]]]]]] # r1107_drfold.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Fri Aug 25 11:28:11 2023 File name: r1107_drfold.pdb no. of DNA/RNA chains: 1 [A=69] no. of nucleotides: 69 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 25 base pair(s) 1 A.C9 A.A10 [C+A] Platform 00-n/a cWH cW+M -158.1(anti) C3'-endo lambda=100.4; -157.2(anti) C2'-exo lambda=58.0 d(C1'-C1')=5.28 d(N1-N9)=4.77 d(C6-C8)=4.75 tor(N1-C1'-C1'-N9)=-0.4 H-bonds[3]: "N3-N6(amino)[3.40]; N3*N7[2.64]; O2'(hydroxyl)-O4'[3.06]" bp_pars: [2.77 1.78 -0.88 -3.53 -7.60 -16.54] 2 A.A10 A.U69 [A-U] WC 20-XX cWW cW-W -157.2(anti) C2'-exo lambda=55.4; -158.0(anti) C3'-endo lambda=59.3 d(C1'-C1')=10.46 d(N1-N9)=8.86 d(C6-C8)=10.09 tor(N1-C1'-C1'-N9)=-5.3 H-bonds[2]: "N1-N3(imino)[3.10]; N6(amino)-O4(carbonyl)[3.58]" bp_pars: [-0.57 0.15 0.22 3.07 -13.50 9.46] 3 A.G11 A.C68 [G-C] WC 19-XIX cWW cW-W -157.3(anti) C2'-exo lambda=57.3; -158.1(anti) C3'-endo lambda=55.6 d(C1'-C1')=10.53 d(N1-N9)=8.89 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-4.3 H-bonds[3]: "N1(imino)-N3[2.99]; N2(amino)-O2(carbonyl)[2.60]; O6(carbonyl)-N4(amino)[3.35]" bp_pars: [-0.21 0.06 0.10 0.74 -13.73 8.67] 4 A.C12 A.G67 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=56.3; -157.2(anti) C2'-exo lambda=56.0 d(C1'-C1')=10.40 d(N1-N9)=8.75 d(C6-C8)=9.92 tor(N1-C1'-C1'-N9)=-3.1 H-bonds[3]: "N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[3.18]; O2(carbonyl)-N2(amino)[2.55]" bp_pars: [0.37 -0.10 -0.06 -2.34 -13.56 8.11] 5 A.A13 A.U66 [A-U] WC 20-XX cWW cW-W -157.2(anti) C2'-exo lambda=56.9; -158.0(anti) C3'-endo lambda=56.7 d(C1'-C1')=10.43 d(N1-N9)=8.81 d(C6-C8)=10.02 tor(N1-C1'-C1'-N9)=-3.3 H-bonds[2]: "N1-N3(imino)[2.97]; N6(amino)-O4(carbonyl)[3.38]" bp_pars: [-0.20 0.07 0.07 2.47 -12.10 8.21] 6 A.G14 A.C65 [G-C] WC 19-XIX cWW cW-W -157.2(anti) C2'-exo lambda=58.3; -158.1(anti) C3'-endo lambda=56.5 d(C1'-C1')=10.34 d(N1-N9)=8.74 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=3.8 H-bonds[3]: "N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[2.53]; O6(carbonyl)-N4(amino)[3.24]" bp_pars: [-0.19 -0.08 -0.60 1.08 -8.67 10.21] 7 A.A15 A.U64 [A-U] WC 20-XX cWW cW-W -157.2(anti) C2'-exo lambda=58.7; -158.0(anti) C2'-exo lambda=57.3 d(C1'-C1')=10.37 d(N1-N9)=8.80 d(C6-C8)=10.02 tor(N1-C1'-C1'-N9)=6.2 H-bonds[2]: "N1-N3(imino)[3.08]; N6(amino)-O4(carbonyl)[3.45]" bp_pars: [-0.08 0.04 -0.96 -0.46 -8.55 10.27] 8 A.A16 A.U63 [A-U] WC 20-XX cWW cW-W -157.3(anti) C2'-exo lambda=53.9; -158.0(anti) C3'-endo lambda=61.0 d(C1'-C1')=10.21 d(N1-N9)=8.63 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=11.0 H-bonds[2]: "N1-N3(imino)[2.98]; N6(amino)-O4(carbonyl)[3.37]" bp_pars: [-0.80 -0.17 -0.85 -5.38 -0.11 8.59] 9 A.G19 A.C22 [G-C] 00-n/a cSW cm-W -157.3(anti) C2'-exo lambda=79.6; -158.1(anti) C3'-endo lambda=74.5 d(C1'-C1')=7.40 d(N1-N9)=6.76 d(C6-C8)=8.54 tor(N1-C1'-C1'-N9)=-25.0 H-bonds[1]: "N1(imino)-N3[3.15]" bp_pars: [0.62 0.08 -0.96 32.57 -38.98 68.50] 10 A.G19 A.C24 [G-C] 00-n/a ... c... -157.3(anti) C2'-exo lambda=161.8; -158.1(anti) C3'-endo lambda=29.7 d(C1'-C1')=3.80 d(N1-N9)=3.94 d(C6-C8)=5.70 tor(N1-C1'-C1'-N9)=39.1 H-bonds[4]: "N2(amino)*N4(amino)[2.48]; N3*N3[2.23]; O2'(hydroxyl)-O2(carbonyl)[2.90]; O2'(hydroxyl)-O4'[2.84]" bp_pars: [3.35 -2.11 -0.02 36.04 6.82 93.22] 11 A.C22 A.A23 [C+A] Platform 00-n/a cSH cm+M -158.1(anti) C3'-endo lambda=126.5; -157.2(anti) C2'-exo lambda=25.3 d(C1'-C1')=5.56 d(N1-N9)=5.22 d(C6-C8)=5.00 tor(N1-C1'-C1'-N9)=-61.0 H-bonds[4]: "O5'*OP2[2.67]; N3-N6(amino)[3.67]; O2(carbonyl)*N7[2.72]; O2'(hydroxyl)-O4'[3.40]" bp_pars: [5.39 -0.75 1.78 -30.97 -35.13 5.51] 12 A.C22 A.C24 [C+C] 00-n/a cWH cW+M -158.1(anti) C3'-endo lambda=94.1; -158.1(anti) C3'-endo lambda=36.3 d(C1'-C1')=8.61 d(N1-N9)=7.55 d(C6-C8)=7.59 tor(N1-C1'-C1'-N9)=-13.7 H-bonds[1]: "O2(carbonyl)-N4(amino)[2.98]" bp_pars: [3.84 0.82 -0.88 -23.90 -26.29 -36.90] 13 A.U26 A.A61 [U-A] 00-n/a cWW cW-W -158.0(anti) C3'-endo lambda=41.3; -157.2(anti) C2'-exo lambda=72.6 d(C1'-C1')=10.02 d(N1-N9)=8.48 d(C6-C8)=9.59 tor(N1-C1'-C1'-N9)=-0.0 H-bonds[2]: "N3(imino)-N1[3.19]; O4(carbonyl)-N6(amino)[3.47]" bp_pars: [-2.48 -0.59 -0.34 19.65 -17.46 7.67] 14 A.C27 A.G60 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=50.7; -157.3(anti) C2'-exo lambda=66.7 d(C1'-C1')=10.33 d(N1-N9)=8.82 d(C6-C8)=10.07 tor(N1-C1'-C1'-N9)=3.8 H-bonds[3]: "N3-N1(imino)[3.08]; N3-N2(amino)[2.49]; O2(carbonyl)-N2(amino)[2.62]" bp_pars: [-1.11 0.02 -0.46 3.90 -7.72 12.70] 15 A.G28 A.C59 [G-C] WC 19-XIX cWW cW-W -157.3(anti) C2'-exo lambda=57.8; -158.1(anti) C3'-endo lambda=59.1 d(C1'-C1')=10.59 d(N1-N9)=9.05 d(C6-C8)=10.30 tor(N1-C1'-C1'-N9)=4.3 H-bonds[3]: "N1(imino)-N3[3.26]; N2(amino)-O2(carbonyl)[2.73]; O6(carbonyl)-N4(amino)[3.70]" bp_pars: [-0.48 0.30 -0.45 1.98 -5.85 12.24] 16 A.C29 A.G58 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=55.0; -157.2(anti) C2'-exo lambda=58.9 d(C1'-C1')=10.30 d(N1-N9)=8.68 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-4.4 H-bonds[3]: "N3-N1(imino)[2.78]; N4(amino)-O6(carbonyl)[3.19]; O2(carbonyl)-N2(amino)[2.34]" bp_pars: [0.01 -0.11 0.15 1.89 -13.52 9.57] 17 A.A30 A.U57 [A-U] WC 20-XX cWW cW-W -157.2(anti) C2'-exo lambda=59.7; -158.0(anti) C3'-endo lambda=57.0 d(C1'-C1')=10.50 d(N1-N9)=8.95 d(C6-C8)=10.22 tor(N1-C1'-C1'-N9)=0.3 H-bonds[2]: "N1-N3(imino)[3.14]; N6(amino)-O4(carbonyl)[3.66]" bp_pars: [0.02 0.31 0.17 3.76 -5.32 11.23] 18 A.G31 A.C56 [G-C] WC 19-XIX cWW cW-W -157.2(anti) C2'-exo lambda=61.9; -158.1(anti) C3'-endo lambda=53.8 d(C1'-C1')=10.15 d(N1-N9)=8.58 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=-2.7 H-bonds[4]: "N1(imino)-N3[2.72]; N2(amino)-N3[2.80]; N2(amino)-O2(carbonyl)[2.27]; O6(carbonyl)-N4(amino)[3.14]" bp_pars: [0.38 -0.17 0.02 4.67 -11.71 11.31] 19 A.C32 A.G55 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=60.0; -157.3(anti) C2'-exo lambda=55.3 d(C1'-C1')=10.06 d(N1-N9)=8.48 d(C6-C8)=9.71 tor(N1-C1'-C1'-N9)=-4.9 H-bonds[3]: "N3-N1(imino)[2.72]; N4(amino)-O6(carbonyl)[3.16]; O2(carbonyl)-N2(amino)[2.33]" bp_pars: [0.73 -0.30 -0.03 -2.51 -16.26 11.39] 20 A.C33 A.G54 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=63.8; -157.2(anti) C2'-exo lambda=55.1 d(C1'-C1')=10.21 d(N1-N9)=8.71 d(C6-C8)=10.00 tor(N1-C1'-C1'-N9)=-3.6 H-bonds[3]: "N3-N1(imino)[3.12]; O2(carbonyl)-N1(imino)[3.22]; O2(carbonyl)-N2(amino)[2.66]" bp_pars: [1.09 0.03 -0.11 -12.54 -14.22 14.69] 21 A.C34 A.U51 [C-U] 00-n/a cWW cW-W -158.1(anti) C3'-endo lambda=52.7; -158.0(anti) C3'-endo lambda=39.8 d(C1'-C1')=11.01 d(N1-N9)=8.98 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=5.2 H-bonds[1]: "N4(amino)-O4(carbonyl)[3.83]" bp_pars: [1.09 -0.00 1.79 40.54 31.23 -8.56] 22 A.U36 A.A49 [U-A] 00-n/a tWW cW-W -158.0(anti) C3'-endo lambda=22.1; -157.2(anti) C2'-exo lambda=33.0 d(C1'-C1')=10.71 d(N1-N9)=8.14 d(C6-C8)=7.80 tor(N1-C1'-C1'-N9)=74.6 H-bonds[1]: "N3(imino)-N1[3.04]" bp_pars: [-0.77 -1.30 -2.33 -5.24 9.49 -61.33] 23 A.U36 A.C50 [U-C] 00-n/a cWW cW-W -158.0(anti) C3'-endo lambda=31.8; -158.0(anti) C3'-endo lambda=52.5 d(C1'-C1')=9.33 d(N1-N9)=7.18 d(C6-C8)=8.01 tor(N1-C1'-C1'-N9)=11.0 H-bonds[1]: "N3(imino)-N3[3.06]" bp_pars: [-1.74 -2.26 0.31 -3.47 12.61 -15.68] 24 A.G37 A.A49 [G-A] 00-n/a cHW cM-W -157.2(anti) C2'-exo lambda=23.1; -157.2(anti) C2'-exo lambda=48.0 d(C1'-C1')=11.23 d(N1-N9)=8.91 d(C6-C8)=8.84 tor(N1-C1'-C1'-N9)=9.9 H-bonds[3]: "N1(imino)-N1[2.51]; N1(imino)-N3[3.34]; O6(carbonyl)-N6(amino)[2.41]" bp_pars: [-2.35 -0.75 0.19 -12.27 14.12 -37.71] 25 A.U38 A.C48 [U-C] 00-n/a c.W c.-W -158.0(anti) C3'-endo lambda=20.3; -158.1(anti) C3'-endo lambda=39.4 d(C1'-C1')=12.84 d(N1-N9)=10.31 d(C6-C8)=10.52 tor(N1-C1'-C1'-N9)=16.1 H-bonds[1]: "O4(carbonyl)-N4(amino)[3.90]" bp_pars: [-2.16 0.81 -0.27 -6.25 2.87 -42.19] **************************************************************************** List of 2 multiplet(s) 1 nts=3 A.C9+A.A10+A.U69 [CAU] 2 nts=3 A.G19+A.C22+A.C24 [GCC] **************************************************************************** List of 3 helices helix=1[1] bps=7 1 A.A10 A.U69 [A-U] WC 20-XX cWW cW-W 2 A.G11 A.C68 [G-C] WC 19-XIX cWW cW-W 3 A.C12 A.G67 [C-G] WC 19-XIX cWW cW-W 4 A.A13 A.U66 [A-U] WC 20-XX cWW cW-W 5 A.G14 A.C65 [G-C] WC 19-XIX cWW cW-W 6 A.A15 A.U64 [A-U] WC 20-XX cWW cW-W 7 A.A16 A.U63 [A-U] WC 20-XX cWW cW-W helix=2[1] bps=8 1 A.U26 A.A61 [U-A] 00-n/a cWW cW-W 2 A.C27 A.G60 [C-G] WC 19-XIX cWW cW-W 3 A.G28 A.C59 [G-C] WC 19-XIX cWW cW-W 4 A.C29 A.G58 [C-G] WC 19-XIX cWW cW-W 5 A.A30 A.U57 [A-U] WC 20-XX cWW cW-W 6 A.G31 A.C56 [G-C] WC 19-XIX cWW cW-W 7 A.C32 A.G55 [C-G] WC 19-XIX cWW cW-W 8 A.C33 A.G54 [C-G] WC 19-XIX cWW cW-W helix=3[0] bps=4 1 A.C34 A.U51 [C-U] 00-n/a cWW cW-W 2 A.U36 A.C50 [U-C] 00-n/a cWW cW-W 3 A.G37 A.A49 [G-A] 00-n/a cHW cM-W 4 A.U38 A.C48 [U-C] 00-n/a c.W c.-W **************************************************************************** List of 2 stems stem=1[#1] bps=7 1 A.A10 A.U69 [A-U] WC 20-XX cWW cW-W 2 A.G11 A.C68 [G-C] WC 19-XIX cWW cW-W 3 A.C12 A.G67 [C-G] WC 19-XIX cWW cW-W 4 A.A13 A.U66 [A-U] WC 20-XX cWW cW-W 5 A.G14 A.C65 [G-C] WC 19-XIX cWW cW-W 6 A.A15 A.U64 [A-U] WC 20-XX cWW cW-W 7 A.A16 A.U63 [A-U] WC 20-XX cWW cW-W stem=2[#2] bps=7 1 A.C27 A.G60 [C-G] WC 19-XIX cWW cW-W 2 A.G28 A.C59 [G-C] WC 19-XIX cWW cW-W 3 A.C29 A.G58 [C-G] WC 19-XIX cWW cW-W 4 A.A30 A.U57 [A-U] WC 20-XX cWW cW-W 5 A.G31 A.C56 [G-C] WC 19-XIX cWW cW-W 6 A.C32 A.G55 [C-G] WC 19-XIX cWW cW-W 7 A.C33 A.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** >chain-A #1 RNA* with 69 nts GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU .........(((((((..........(((((((....................)))))))..))))))) # r1107_drfold_ss.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Fri Aug 25 11:28:11 2023 File name: r1107_drfold_ss.pdb no. of DNA/RNA chains: 1 [A=69] no. of nucleotides: 69 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 16 base pair(s) 1 A.A8 A.G67 [A-G] 00-n/a cWS cW-m -157.2(anti) C2'-exo lambda=88.2; -157.2(anti) C2'-exo lambda=103.7 d(C1'-C1')=6.67 d(N1-N9)=7.00 d(C6-C8)=9.30 tor(N1-C1'-C1'-N9)=-25.3 H-bonds[3]: "N1-N1(imino)[2.34]; N3*N3[2.54]; N6(amino)*N2(amino)[3.12]" bp_pars: [-0.69 2.34 0.84 24.01 -25.29 88.96] 2 A.C9 A.G67 [C-G] 00-n/a cWS cW-m -158.1(anti) C3'-endo lambda=114.5; -157.2(anti) C2'-exo lambda=108.2 d(C1'-C1')=4.47 d(N1-N9)=5.61 d(C6-C8)=8.19 tor(N1-C1'-C1'-N9)=-35.4 H-bonds[3]: "N3-N2(amino)[2.95]; O2(carbonyl)-N1(imino)[3.27]; O2'(hydroxyl)-O4'[3.36]" bp_pars: [0.72 3.93 2.03 34.88 -31.04 127.48] 3 A.G11 A.U36 [G-U] 00-n/a cWW cW-W -157.2(anti) C2'-exo lambda=55.2; -158.0(anti) C3'-endo lambda=62.7 d(C1'-C1')=10.90 d(N1-N9)=9.38 d(C6-C8)=10.59 tor(N1-C1'-C1'-N9)=17.4 H-bonds[1]: "N2(amino)-O2(carbonyl)[3.53]" bp_pars: [-1.44 0.89 0.82 31.91 26.72 14.71] 4 A.A13 A.C34 [A-C] 00-n/a ... c... -157.2(anti) C2'-exo lambda=52.5; -158.1(anti) C3'-endo lambda=67.9 d(C1'-C1')=10.47 d(N1-N9)=9.01 d(C6-C8)=10.32 tor(N1-C1'-C1'-N9)=-1.4 H-bonds[1]: "N1*O2(carbonyl)[3.19]" bp_pars: [-1.73 0.34 -0.01 8.64 -9.79 16.27] 5 A.A13 A.U64 [A-U] 00-n/a cHH cM-M -157.2(anti) C2'-exo lambda=65.3; -158.0(anti) C3'-endo lambda=39.1 d(C1'-C1')=7.39 d(N1-N9)=5.64 d(C6-C8)=3.65 tor(N1-C1'-C1'-N9)=10.4 H-bonds[4]: "O5'*OP2[2.39]; N6(amino)-O4(carbonyl)[3.27]; N7-N3(imino)[3.25]; OP1*O5'[2.94]" bp_pars: [1.71 -5.00 1.51 -39.91 -38.98 149.97] 6 A.G14 A.C33 [G-C] WC 19-XIX cWW cW-W -157.2(anti) C2'-exo lambda=60.5; -158.1(anti) C3'-endo lambda=63.3 d(C1'-C1')=10.93 d(N1-N9)=9.54 d(C6-C8)=10.95 tor(N1-C1'-C1'-N9)=-3.5 H-bonds[2]: "N1(imino)-N3[3.86]; N2(amino)-O2(carbonyl)[3.04]" bp_pars: [-0.63 1.04 0.04 4.04 -12.08 19.59] 7 A.A16 A.G31 [A-G] 08-VIII cWW cW-W -157.2(anti) C2'-exo lambda=75.5; -157.2(anti) C2'-exo lambda=58.5 d(C1'-C1')=10.72 d(N1-N9)=9.58 d(C6-C8)=10.93 tor(N1-C1'-C1'-N9)=-2.1 H-bonds[3]: "N1-N1(imino)[2.67]; N3-N1(imino)[3.42]; N3-N2(amino)[2.98]" bp_pars: [1.58 1.18 0.66 -4.15 -3.43 25.14] 8 A.G17 A.C29 [G-C] WC 19-XIX cWW cW-W -157.3(anti) C2'-exo lambda=61.5; -158.1(anti) C3'-endo lambda=47.2 d(C1'-C1')=10.72 d(N1-N9)=9.01 d(C6-C8)=10.08 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[4]: "N1(imino)-N3[3.12]; N2(amino)-N3[2.91]; N2(amino)-O2(carbonyl)[2.95]; O6(carbonyl)-N4(amino)[3.24]" bp_pars: [1.00 0.10 0.17 16.31 -9.52 3.63] 9 A.C18 A.G28 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=56.0; -157.3(anti) C2'-exo lambda=56.0 d(C1'-C1')=10.67 d(N1-N9)=9.02 d(C6-C8)=10.14 tor(N1-C1'-C1'-N9)=6.8 H-bonds[3]: "N3-N1(imino)[3.15]; N4(amino)-O6(carbonyl)[3.37]; O2(carbonyl)-N2(amino)[2.82]" bp_pars: [0.31 0.11 -0.75 7.60 -6.46 6.87] 10 A.G19 A.C27 [G-C] WC 19-XIX cWW cW-W -157.3(anti) C2'-exo lambda=59.1; -158.1(anti) C3'-endo lambda=54.3 d(C1'-C1')=10.12 d(N1-N9)=8.50 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=-0.3 H-bonds[3]: "N1(imino)-N3[2.68]; N2(amino)-O2(carbonyl)[2.51]; O6(carbonyl)-N4(amino)[2.91]" bp_pars: [0.10 -0.35 -0.57 5.56 -14.98 9.49] 11 A.C35 A.U36 [C+U] Platform 00-n/a cWH cW+M -158.1(anti) C3'-endo lambda=75.9; -158.0(anti) C3'-endo lambda=67.7 d(C1'-C1')=5.53 d(N1-N9)=4.61 d(C6-C8)=4.16 tor(N1-C1'-C1'-N9)=1.8 H-bonds[2]: "N3-N3(imino)[3.40]; O4'*OP2[2.45]" bp_pars: [0.25 2.31 -1.86 5.67 -22.15 -34.24] 12 A.C39 A.G58 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=55.1; -157.3(anti) C2'-exo lambda=59.3 d(C1'-C1')=10.83 d(N1-N9)=9.23 d(C6-C8)=10.42 tor(N1-C1'-C1'-N9)=-2.4 H-bonds[3]: "N3-N1(imino)[3.34]; N4(amino)-O6(carbonyl)[3.70]; O2(carbonyl)-N2(amino)[2.96]" bp_pars: [-0.03 0.43 -0.35 7.87 -15.99 10.12] 13 A.A40 A.U57 [A-U] WC 20-XX cWW cW-W -157.2(anti) C2'-exo lambda=52.2; -158.0(anti) C2'-exo lambda=60.6 d(C1'-C1')=10.36 d(N1-N9)=8.73 d(C6-C8)=9.87 tor(N1-C1'-C1'-N9)=1.1 H-bonds[2]: "N1-N3(imino)[3.12]; N6(amino)-O4(carbonyl)[3.35]" bp_pars: [-0.97 -0.14 -0.70 3.62 -14.14 7.76] 14 A.G41 A.C56 [G-C] WC 19-XIX cWW cW-W -157.2(anti) C2'-exo lambda=54.1; -158.1(anti) C3'-endo lambda=57.7 d(C1'-C1')=10.55 d(N1-N9)=8.90 d(C6-C8)=10.03 tor(N1-C1'-C1'-N9)=1.4 H-bonds[3]: "N1(imino)-N3[3.12]; N2(amino)-O2(carbonyl)[2.92]; O6(carbonyl)-N4(amino)[3.31]" bp_pars: [-0.68 -0.03 -0.61 3.42 -12.84 7.62] 15 A.C42 A.G55 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=53.4; -157.2(anti) C2'-exo lambda=55.6 d(C1'-C1')=10.51 d(N1-N9)=8.79 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-2.8 H-bonds[3]: "N3-N1(imino)[2.84]; N4(amino)-O6(carbonyl)[3.01]; O2(carbonyl)-N2(amino)[2.67]" bp_pars: [0.15 -0.15 -0.16 -1.29 -14.60 4.83] 16 A.C43 A.G54 [C-G] WC 19-XIX cWW cW-W -158.1(anti) C3'-endo lambda=53.3; -157.2(anti) C2'-exo lambda=69.0 d(C1'-C1')=10.11 d(N1-N9)=8.71 d(C6-C8)=10.13 tor(N1-C1'-C1'-N9)=21.4 H-bonds[3]: "N3-N1(imino)[3.12]; N3-N2(amino)[2.34]; O2(carbonyl)-N2(amino)[2.39]" bp_pars: [-1.00 0.16 -0.60 -2.46 19.43 19.14] **************************************************************************** List of 1 multiplet(s) 1 nts=3 A.A13+A.C34+A.U64 [ACU] **************************************************************************** List of 3 helices helix=1[0] bps=2 1 A.A13 A.C34 [A-C] 00-n/a ... c... 2 A.G14 A.C33 [G-C] WC 19-XIX cWW cW-W helix=2[1] bps=4 1 A.A16 A.G31 [A-G] 08-VIII cWW cW-W 2 A.G17 A.C29 [G-C] WC 19-XIX cWW cW-W 3 A.C18 A.G28 [C-G] WC 19-XIX cWW cW-W 4 A.G19 A.C27 [G-C] WC 19-XIX cWW cW-W helix=3[1] bps=5 1 A.C39 A.G58 [C-G] WC 19-XIX cWW cW-W 2 A.A40 A.U57 [A-U] WC 20-XX cWW cW-W 3 A.G41 A.C56 [G-C] WC 19-XIX cWW cW-W 4 A.C42 A.G55 [C-G] WC 19-XIX cWW cW-W 5 A.C43 A.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems stem=1[#2] bps=3 1 A.G17 A.C29 [G-C] WC 19-XIX cWW cW-W 2 A.C18 A.G28 [C-G] WC 19-XIX cWW cW-W 3 A.G19 A.C27 [G-C] WC 19-XIX cWW cW-W stem=2[#3] bps=5 1 A.C39 A.G58 [C-G] WC 19-XIX cWW cW-W 2 A.A40 A.U57 [A-U] WC 20-XX cWW cW-W 3 A.G41 A.C56 [G-C] WC 19-XIX cWW cW-W 4 A.C42 A.G55 [C-G] WC 19-XIX cWW cW-W 5 A.C43 A.G54 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 A.G14 A.C33 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 2 hairpin loop(s) 1 nts=7 UUCACGU closed by pair {A.G19+A.C27 [GC], #1} A.G19+A.U20+A.U21+A.C22+A.A23+A.C24+A.G25+A.U26+A.C27 [GUUCACGUC] 2 nts=10 AUUGCACUCC closed by pair {A.C43+A.G54 [CG], #2} A.C43+A.A44+A.U45+A.U46+A.G47+A.C48+A.A49+A.C50+A.U51+A.C52+A.C53+A.G54 [CAUUGCACUCCG] **************************************************************************** List of 1 internal loop(s) 1 asymmetric internal loop: 9 nts; [2x3]; linked by [#-1, #1] A.G14+A.A15+A.A16+A.G17+A.C29+A.A30+A.G31+A.C32+A.C33 [GAAGCAGCC] **************************************************************************** >chain-A #1 RNA* with 69 nts GGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGCCAUUGCACUCCGGCUGCGAAUUCUGCU .............(..(((.......)))...).....(((((..........)))))........... DONE!