# APC52model1.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: Sun Feb 25 08:17:37 2024 File name: APC52model1.pdb no. of DNA/RNA chains: 1 [A=52] no. of nucleotides: 52 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 13 base pair(s) 1 A.C2 A.G51 [C-G] WC 19-XIX cWW cW-W -166.5(anti) C3'-endo lambda=51.1; -171.6(anti) C3'-endo lambda=50.8 d(C1'-C1')=10.94 d(N1-N9)=9.08 d(C6-C8)=9.89 tor(N1-C1'-C1'-N9)=-11.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.92]; N3-N1(imino)[2.97]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.19 -0.11 0.01 5.97 -8.31 -3.99] 2 A.C3 A.G50 [C-G] WC 19-XIX cWW cW-W -163.5(anti) C3'-endo lambda=49.5; -165.2(anti) C3'-endo lambda=47.8 d(C1'-C1')=11.08 d(N1-N9)=9.12 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-8.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.95]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.77]" bp_pars: [0.12 -0.14 -0.11 2.89 -7.45 -5.91] 3 A.U4 A.A49 [U-A] WC 20-XX cWW cW-W -164.0(anti) C3'-endo lambda=49.7; -166.2(anti) C3'-endo lambda=48.3 d(C1'-C1')=11.06 d(N1-N9)=9.11 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-9.6 H-bonds[2]: "N3(imino)-N1[2.95]; O4(carbonyl)-N6(amino)[2.78]" bp_pars: [0.07 -0.08 -0.15 0.11 -8.69 -8.13] 4 A.C5 A.G48 [C-G] WC 19-XIX cWW cW-W -164.0(anti) C3'-endo lambda=52.1; -167.7(anti) C3'-endo lambda=52.2 d(C1'-C1')=10.91 d(N1-N9)=9.08 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-9.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.85]; N3-N1(imino)[2.95]; N4(amino)-O6(carbonyl)[2.90]" bp_pars: [0.05 -0.08 -0.03 -0.67 -7.30 -1.80] 5 A.C6 A.U47 [C-U] 00-n/a cWW cW-W -171.3(anti) C3'-endo lambda=44.1; -163.3(anti) C3'-endo lambda=34.9 d(C1'-C1')=11.38 d(N1-N9)=9.08 d(C6-C8)=9.46 tor(N1-C1'-C1'-N9)=-6.4 H-bonds[1]: "N4(amino)-O4(carbonyl)[2.83]" bp_pars: [0.99 -0.39 -0.63 -8.31 -16.48 -28.26] 6 A.U7 A.A46 [U-A] WC 20-XX cWW cW-W -168.0(anti) C3'-endo lambda=50.9; -138.0(anti) C3'-endo lambda=48.8 d(C1'-C1')=10.97 d(N1-N9)=9.07 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-28.3 H-bonds[2]: "N3(imino)-N1[3.07]; O4(carbonyl)-N6(amino)[2.86]" bp_pars: [-0.18 0.03 -0.13 -20.60 -35.74 -7.24] 7 A.A8 A.U45 [A-U] WC 20-XX cWW cW-W -160.3(anti) C3'-endo lambda=57.4; -128.5(anti) C4'-exo lambda=48.6 d(C1'-C1')=10.64 d(N1-N9)=8.86 d(C6-C8)=9.64 tor(N1-C1'-C1'-N9)=-24.5 H-bonds[2]: "N1-N3(imino)[3.08]; N6(amino)-O4(carbonyl)[3.50]" bp_pars: [0.10 0.28 0.29 -40.52 -33.46 -3.90] 8 A.U11 A.G23 [U-G] 00-n/a c.. c.-. -161.6(anti) C3'-endo lambda=17.4; -167.7(anti) C3'-endo lambda=91.3 d(C1'-C1')=12.17 d(N1-N9)=10.84 d(C6-C8)=11.49 tor(N1-C1'-C1'-N9)=-4.5 H-bonds[1]: "O4(carbonyl)-N2(amino)[3.18]" bp_pars: [-7.08 -0.50 1.12 40.45 -4.44 -4.31] 9 A.A13 A.U21 [A-U] WC 20-XX cWW cW-W -162.4(anti) C4'-exo lambda=48.8; -171.2(anti) C3'-endo lambda=49.5 d(C1'-C1')=11.01 d(N1-N9)=9.07 d(C6-C8)=9.84 tor(N1-C1'-C1'-N9)=-16.1 H-bonds[2]: "N1-N3(imino)[2.94]; N6(amino)-O4(carbonyl)[2.84]" bp_pars: [0.04 -0.08 -0.21 5.95 -22.69 -5.62] 10 A.G14 A.C20 [G-C] WC 19-XIX cWW cW-W -140.2(anti) O4'-endo lambda=50.6; -163.1(anti) C3'-endo lambda=49.7 d(C1'-C1')=10.99 d(N1-N9)=9.08 d(C6-C8)=9.86 tor(N1-C1'-C1'-N9)=-2.3 H-bonds[3]: "N1(imino)-N3[2.90]; N2(amino)-O2(carbonyl)[2.88]; O6(carbonyl)-N4(amino)[2.77]" bp_pars: [0.05 -0.14 0.02 4.41 -2.93 -4.75] 11 A.U27 A.C30 [U-C] 00-n/a cH. cM-. -111.3(anti) C2'-exo lambda=23.7; -94.2(anti) C3'-endo lambda=18.2 d(C1'-C1')=13.43 d(N1-N9)=10.65 d(C6-C8)=9.04 tor(N1-C1'-C1'-N9)=29.3 H-bonds[1]: "O4(carbonyl)-N4(amino)[3.38]" bp_pars: [-1.45 4.36 -0.55 42.25 -4.95 -122.78] 12 A.C31 A.G40 [C-G] 00-n/a cW. cW-. -95.0(anti) C3'-endo lambda=100.0; -114.0(anti) C3'-endo lambda=102.9 d(C1'-C1')=7.93 d(N1-N9)=8.52 d(C6-C8)=11.05 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[1]: "O2(carbonyl)-N2(amino)[2.84]" bp_pars: [-0.28 4.25 0.08 5.01 -6.64 94.94] 13 A.C32 A.G39 [C-G] 00-n/a cW. cW-. -101.3(anti) C3'-endo lambda=96.0; -101.7(anti) C3'-endo lambda=102.1 d(C1'-C1')=8.19 d(N1-N9)=8.66 d(C6-C8)=11.14 tor(N1-C1'-C1'-N9)=-12.7 H-bonds[1]: "O2(carbonyl)-N2(amino)[2.91]" bp_pars: [-0.38 4.13 0.16 6.89 -9.58 91.49] **************************************************************************** List of 3 helices helix=1[2] bps=7 1 A.C2 A.G51 [C-G] WC 19-XIX cWW cW-W 2 A.C3 A.G50 [C-G] WC 19-XIX cWW cW-W 3 A.U4 A.A49 [U-A] WC 20-XX cWW cW-W 4 A.C5 A.G48 [C-G] WC 19-XIX cWW cW-W 5 A.C6 A.U47 [C-U] 00-n/a cWW cW-W 6 A.U7 A.A46 [U-A] WC 20-XX cWW cW-W 7 A.A8 A.U45 [A-U] WC 20-XX cWW cW-W helix=2[1] bps=2 1 A.A13 A.U21 [A-U] WC 20-XX cWW cW-W 2 A.G14 A.C20 [G-C] WC 19-XIX cWW cW-W helix=3[0] bps=2 1 A.C31 A.G40 [C-G] 00-n/a cW. cW-. 2 A.C32 A.G39 [C-G] 00-n/a cW. cW-. **************************************************************************** List of 3 stems stem=1[#1] bps=4 1 A.C2 A.G51 [C-G] WC 19-XIX cWW cW-W 2 A.C3 A.G50 [C-G] WC 19-XIX cWW cW-W 3 A.U4 A.A49 [U-A] WC 20-XX cWW cW-W 4 A.C5 A.G48 [C-G] WC 19-XIX cWW cW-W stem=2[#1] bps=2 1 A.U7 A.A46 [U-A] WC 20-XX cWW cW-W 2 A.A8 A.U45 [A-U] WC 20-XX cWW cW-W stem=3[#2] bps=2 1 A.A13 A.U21 [A-U] WC 20-XX cWW cW-W 2 A.G14 A.C20 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack(s) 1 Helix#1 contains 2 stems: [#1, #2] **************************************************************************** List of 1 hairpin loop(s) 1 nts=5 CUGUA closed by pair {A.G14+A.C20 [GC], #3} A.G14+A.C15+A.U16+A.G17+A.U18+A.A19+A.C20 [GCUGUAC] **************************************************************************** List of 2 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#1, #2] A.C5+A.C6+A.U7+A.A46+A.U47+A.G48 [CCUAUG] 2 asymmetric internal loop: 31 nts; [4x23]; linked by [#2, #3] A.A8+A.A9+A.C10+A.U11+A.G12+A.A13+A.U21+A.C22+A.G23+A.A24+A.C25+A.U26+A.U27+A.A28+A.U29+A.C30+A.C31+A.C32+A.G33+A.G34+A.A35+A.U36+A.G37+A.G38+A.G39+A.G40+A.C41+A.U42+A.C43+A.U44+A.U45 [AACUGAUCGACUUAUCCCGGAUGGGGCUCUU] **************************************************************************** >chain-A #1 RNA with 52 nts GCCUCCUAACUGAGCUGUACUCGACUUAUCCCGGAUGGGGCUCUUAUGAGGC .((((.((....((.....)).......................)).)))). DONE!