# RNA_SS_NO_RESTRAINTS-10fd39c4_sim_minE_TOTAL-000001_AA.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 Mar 29 12:51:51 2024 File name: RNA_SS_NO_RESTRAINTS-10fd39c4_sim_minE_TOTAL-000001_AA.pdb no. of DNA/RNA chains: 1 [A=33] no. of nucleotides: 33 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 16 base pair(s) 1 A.G1 A.C33 [G-C] WC 19-XIX cWW cW-W -171.7(anti) C3'-endo lambda=50.2; -169.9(anti) C3'-endo lambda=60.5 d(C1'-C1')=10.34 d(N1-N9)=8.73 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-7.2 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.17]; N1(imino)-N3[2.92]; N2(amino)-O2(carbonyl)[2.60]" bp_pars: [-0.98 -0.27 -0.24 0.52 -7.22 6.82] 2 A.G2 A.U32 [G-U] 00-n/a cWW cW-W -160.9(anti) C3'-endo lambda=55.0; -174.5(anti) C3'-endo lambda=53.7 d(C1'-C1')=10.85 d(N1-N9)=9.10 d(C6-C8)=10.10 tor(N1-C1'-C1'-N9)=-2.2 H-bonds[2]: "N1(imino)*N3(imino)[3.32]; N2(amino)-O2(carbonyl)[3.00]" bp_pars: [-0.87 0.05 -0.44 -5.00 -8.55 2.89] 3 A.C3 A.G31 [C-G] WC 19-XIX cWW cW-W -163.8(anti) C3'-endo lambda=50.0; -175.1(anti) C3'-endo lambda=45.7 d(C1'-C1')=11.27 d(N1-N9)=9.29 d(C6-C8)=10.02 tor(N1-C1'-C1'-N9)=-6.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.45]; N3-N1(imino)[3.23]; N4(amino)-O6(carbonyl)[2.89]" bp_pars: [0.54 0.00 -0.32 2.18 -2.17 -8.54] 4 A.G4 A.C30 [G-C] WC 19-XIX cWW cW-W 178.1(anti) C3'-endo lambda=49.0; -161.1(anti) C3'-endo lambda=50.7 d(C1'-C1')=11.38 d(N1-N9)=9.42 d(C6-C8)=10.20 tor(N1-C1'-C1'-N9)=-0.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.99]; N1(imino)-N3[3.25]; N2(amino)-O2(carbonyl)[3.39]" bp_pars: [0.13 0.20 -0.13 -6.67 0.70 -6.70] 5 A.A5 A.G29 [A-G] 08-VIII cWW cW-W -165.8(anti) C3'-endo lambda=55.0; -168.5(anti) C3'-endo lambda=45.3 d(C1'-C1')=11.45 d(N1-N9)=9.61 d(C6-C8)=10.17 tor(N1-C1'-C1'-N9)=-8.1 H-bonds[2]: "N6(amino)-O6(carbonyl)[2.20]; N3-N1(imino)[3.67]" bp_pars: [1.03 0.30 -0.58 -7.28 -21.63 -8.93] 6 A.U6 A.C27 [U-C] 00-n/a cWW cW-W -168.7(anti) C3'-endo lambda=32.3; -154.9(anti) C3'-endo lambda=39.5 d(C1'-C1')=13.12 d(N1-N9)=10.58 d(C6-C8)=10.72 tor(N1-C1'-C1'-N9)=7.3 H-bonds[1]: "O4(carbonyl)-N4(amino)[3.98]" bp_pars: [0.57 0.90 -2.44 4.17 -23.84 -35.56] 7 A.U6 A.A28 [U-A] WC 20-XX cWW cW-W -168.7(anti) C3'-endo lambda=54.3; -156.5(anti) C3'-endo lambda=53.8 d(C1'-C1')=10.63 d(N1-N9)=8.87 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-18.2 H-bonds[2]: "N3(imino)-N1[2.93]; O4(carbonyl)-N6(amino)[3.16]" bp_pars: [0.42 -0.07 0.27 -1.93 -8.68 3.21] 8 A.A7 A.C27 [A-C] 00-n/a ... c... -163.5(anti) C3'-endo lambda=55.5; -154.9(anti) C3'-endo lambda=54.4 d(C1'-C1')=10.30 d(N1-N9)=8.58 d(C6-C8)=9.46 tor(N1-C1'-C1'-N9)=-14.7 H-bonds[2]: "N6(amino)*N4(amino)[2.66]; N1*N3[2.40]" bp_pars: [0.47 -0.51 0.04 4.10 -36.19 -0.37] 9 A.C8 A.G26 [C-G] WC 19-XIX cWW cW-W -166.8(anti) C3'-endo lambda=51.6; -167.1(anti) C3'-endo lambda=48.4 d(C1'-C1')=10.22 d(N1-N9)=8.34 d(C6-C8)=9.16 tor(N1-C1'-C1'-N9)=-9.8 H-bonds[2]: "O2(carbonyl)-N2(amino)[2.37]; N3-N1(imino)[2.21]" bp_pars: [-0.14 -0.84 -0.05 -7.68 -11.19 -4.56] 10 A.C9 A.G25 [C-G] WC 19-XIX cWW cW-W -156.5(anti) C3'-endo lambda=53.6; -171.3(anti) C3'-endo lambda=64.0 d(C1'-C1')=10.07 d(N1-N9)=8.54 d(C6-C8)=9.58 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[2]: "N3-N1(imino)[2.53]; N4(amino)-O6(carbonyl)[2.75]" bp_pars: [-0.41 -0.43 0.31 7.71 -7.20 4.71] 11 A.A10 A.U24 [A-U] WC 20-XX cWW cW-W -155.3(anti) C3'-endo lambda=63.4; -147.3(anti) C3'-endo lambda=60.9 d(C1'-C1')=9.81 d(N1-N9)=8.42 d(C6-C8)=9.73 tor(N1-C1'-C1'-N9)=4.0 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.50]; N1-N3(imino)[2.65]" bp_pars: [0.01 -0.10 -0.31 5.40 19.21 16.87] 12 A.G11 A.C20 [G-C] 00-n/a cWW cW-W -169.0(anti) C3'-endo lambda=43.9; -152.5(anti) C3'-endo lambda=47.0 d(C1'-C1')=12.02 d(N1-N9)=9.92 d(C6-C8)=10.43 tor(N1-C1'-C1'-N9)=-5.4 H-bonds[2]: "O6(carbonyl)-N4(amino)[3.13]; N1(imino)-N3[3.94]" bp_pars: [-0.28 0.54 -0.96 13.52 -21.32 -15.77] 13 A.G11 A.C21 [G-C] WC 19-XIX cWW cW-W -169.0(anti) C3'-endo lambda=60.0; -152.7(anti) C3'-endo lambda=61.8 d(C1'-C1')=10.36 d(N1-N9)=8.89 d(C6-C8)=10.14 tor(N1-C1'-C1'-N9)=1.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.64]; N1(imino)-N3[3.05]; N2(amino)-O2(carbonyl)[2.35]" bp_pars: [-0.25 0.20 0.28 -5.51 -3.77 14.38] 14 A.C12 A.G19 [C-G] WC 19-XIX cWW cW-W -170.2(anti) C3'-endo lambda=47.6; -172.6(anti) C3'-endo lambda=52.8 d(C1'-C1')=10.92 d(N1-N9)=9.08 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=-11.5 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.99]; N3-N1(imino)[2.94]; N4(amino)-O6(carbonyl)[2.88]" bp_pars: [-0.27 -0.06 -0.19 7.01 -16.14 -1.88] 15 A.C13 A.G18 [C-G] WC 19-XIX cWW cW-W -169.6(anti) C3'-endo lambda=58.5; -162.0(anti) C3'-endo lambda=57.5 d(C1'-C1')=10.67 d(N1-N9)=9.06 d(C6-C8)=10.26 tor(N1-C1'-C1'-N9)=-5.7 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.56]; N3-N1(imino)[3.15]; N4(amino)-O6(carbonyl)[3.65]" bp_pars: [0.15 0.28 -0.26 1.63 7.54 11.79] 16 A.G14 A.A17 [G-A] Sheared 11-XI tSH cm-M -164.4(anti) C3'-endo lambda=83.0; -161.2(anti) C3'-endo lambda=11.1 d(C1'-C1')=9.83 d(N1-N9)=8.39 d(C6-C8)=8.47 tor(N1-C1'-C1'-N9)=-79.4 H-bonds[2]: "N2(amino)-N7[2.22]; N3-N6(amino)[3.50]" bp_pars: [6.37 -4.18 1.14 22.45 25.68 -24.07] **************************************************************************** List of 1 helix helix=1[3] bps=14 1 A.G1 A.C33 [G-C] WC 19-XIX cWW cW-W 2 A.G2 A.U32 [G-U] 00-n/a cWW cW-W 3 A.C3 A.G31 [C-G] WC 19-XIX cWW cW-W 4 A.G4 A.C30 [G-C] WC 19-XIX cWW cW-W 5 A.A5 A.G29 [A-G] 08-VIII cWW cW-W 6 A.U6 A.A28 [U-A] WC 20-XX cWW cW-W 7 A.A7 A.C27 [A-C] 00-n/a ... c... 8 A.C8 A.G26 [C-G] WC 19-XIX cWW cW-W 9 A.C9 A.G25 [C-G] WC 19-XIX cWW cW-W 10 A.A10 A.U24 [A-U] WC 20-XX cWW cW-W 11 A.G11 A.C21 [G-C] WC 19-XIX cWW cW-W 12 A.C12 A.G19 [C-G] WC 19-XIX cWW cW-W 13 A.C13 A.G18 [C-G] WC 19-XIX cWW cW-W 14 A.G14 A.A17 [G-A] Sheared 11-XI tSH cm-M **************************************************************************** List of 3 stems stem=1[#1] bps=2 1 A.C3 A.G31 [C-G] WC 19-XIX cWW cW-W 2 A.G4 A.C30 [G-C] WC 19-XIX cWW cW-W stem=2[#1] bps=3 1 A.C8 A.G26 [C-G] WC 19-XIX cWW cW-W 2 A.C9 A.G25 [C-G] WC 19-XIX cWW cW-W 3 A.A10 A.U24 [A-U] WC 20-XX cWW cW-W stem=3[#1] bps=2 1 A.C12 A.G19 [C-G] WC 19-XIX cWW cW-W 2 A.C13 A.G18 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 3 lone WC/wobble pair(s) -1 A.G1 A.C33 [G-C] WC 19-XIX cWW cW-W -2 A.U6 A.A28 [U-A] WC 20-XX cWW cW-W -3 A.G11 A.C21 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 3 stems: [#1, #2, #3] **************************************************************************** List of 1 hairpin loop(s) 1 nts=4 GAAA closed by pair {A.C13+A.G18 [CG], #3} A.C13+A.G14+A.A15+A.A16+A.A17+A.G18 [CGAAAG] **************************************************************************** List of 3 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#-1, #1] A.G1+A.G2+A.C3+A.G31+A.U32+A.C33 [GGCGUC] 2 symmetric internal loop: 6 nts; [1x1]; linked by [#1, #-2] A.G4+A.A5+A.U6+A.A28+A.G29+A.C30 [GAUAGC] 3 symmetric internal loop: 6 nts; [1x1]; linked by [#-2, #2] A.U6+A.A7+A.C8+A.G26+A.C27+A.A28 [UACGCA] **************************************************************************** List of 1 junction(s) 1* 3-way junctions: 11 nts; [0x4x1]; linked by [#-3, #3, #3] A.G11+A.C12+A.C13+A.G14+A.A15+A.A16+A.A17+A.G18+A.G19+A.C20+A.C21 [GCCGAAAGGCC] **************************************************************************** >chain-A #1 RNA with 33 nts GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC (.((.(.((((((....)).)..))).).)).) DONE!