# Composer-3-3_GCGA.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: Mon Dec 4 19:27:19 2023 File name: Composer-3-3_GCGA.pdb no. of DNA/RNA chains: 1 [A=47] no. of nucleotides: 47 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 17 base pair(s) 1 1:A.G1 1:A.C47 [G-C] WC 19-XIX cWW cW-W -177.4(anti) C2'-exo lambda=46.2; -178.4(anti) C3'-endo lambda=57.6 d(C1'-C1')=10.59 d(N1-N9)=8.79 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=0.4 H-bonds[4]: "N2(amino)-O2(carbonyl)[3.02]; N1(imino)-O2(carbonyl)[3.11]; N1(imino)-N3[2.98]; O6(carbonyl)-N4(amino)[2.83]" bp_pars: [-1.11 -0.43 -0.21 -10.00 -1.11 -4.20] 2 1:A.G2 1:A.C46 [G-C] WC 19-XIX cWW cW-W -165.9(anti) C3'-endo lambda=50.4; -153.1(anti) C3'-endo lambda=58.1 d(C1'-C1')=10.48 d(N1-N9)=8.78 d(C6-C8)=9.71 tor(N1-C1'-C1'-N9)=-3.2 H-bonds[3]: "N2(amino)-O2(carbonyl)[2.72]; N1(imino)-N3[2.86]; O6(carbonyl)-N4(amino)[2.88]" bp_pars: [-0.80 -0.34 0.02 -1.26 -3.54 0.54] 3 1:A.A3 1:A.U45 [A-U] WC 20-XX cWW cW-W -155.0(anti) C3'-endo lambda=58.3; -154.2(anti) C3'-endo lambda=58.4 d(C1'-C1')=10.15 d(N1-N9)=8.61 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-1.0 H-bonds[2]: "N1-N3(imino)[2.67]; N6(amino)-O4(carbonyl)[3.01]" bp_pars: [0.01 -0.21 -0.16 -2.48 -2.99 6.98] 4 1:A.U4 1:A.A44 [U-A] WC 20-XX cWW cW-W -153.0(anti) C3'-endo lambda=56.3; -157.6(anti) C3'-endo lambda=56.0 d(C1'-C1')=10.34 d(N1-N9)=8.71 d(C6-C8)=9.72 tor(N1-C1'-C1'-N9)=-1.8 H-bonds[2]: "N3(imino)-N1[2.69]; O4(carbonyl)-N6(amino)[2.86]" bp_pars: [0.02 -0.23 0.00 -0.05 -2.06 2.59] 5 1:A.C5 1:A.G43 [C-G] WC 19-XIX cWW cW-W -174.2(anti) C3'-endo lambda=58.8; -170.8(anti) C3'-endo lambda=50.4 d(C1'-C1')=10.39 d(N1-N9)=8.70 d(C6-C8)=9.64 tor(N1-C1'-C1'-N9)=-3.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.68]; N3-N1(imino)[2.83]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.88 -0.40 -0.12 8.39 -4.99 0.86] 6 1:A.A6 1:A.U42 [A-U] WC 20-XX cWW cW-W 179.7(anti) C2'-exo lambda=53.3; -160.2(anti) C3'-endo lambda=49.7 d(C1'-C1')=10.77 d(N1-N9)=8.95 d(C6-C8)=9.75 tor(N1-C1'-C1'-N9)=5.3 H-bonds[2]: "N1-N3(imino)[2.84]; N6(amino)-O4(carbonyl)[2.66]" bp_pars: [0.33 -0.17 -0.35 8.14 2.15 -6.71] 7 1:A.C7 1:A.A21 [C-A] 00-n/a tHW cM-W -160.1(anti) C2'-exo lambda=24.3; -158.4(anti) C2'-exo lambda=58.4 d(C1'-C1')=11.92 d(N1-N9)=9.87 d(C6-C8)=9.80 tor(N1-C1'-C1'-N9)=62.8 H-bonds[1]: "N4(amino)-N1[3.06]" bp_pars: [-5.10 -0.71 -1.87 32.20 3.45 -43.38] 8 1:A.U9 1:A.A20 [U-A] WC 20-XX cWW cW-W -162.5(anti) C3'-endo lambda=51.1; -176.6(anti) C3'-endo lambda=51.5 d(C1'-C1')=10.80 d(N1-N9)=8.97 d(C6-C8)=9.77 tor(N1-C1'-C1'-N9)=-6.9 H-bonds[2]: "N3(imino)-N1[2.85]; O4(carbonyl)-N6(amino)[2.68]" bp_pars: [-0.04 -0.16 0.01 1.89 -9.40 -6.55] 9 1:A.G10 1:A.C19 [G-C] WC 19-XIX cWW cW-W -164.9(anti) C3'-endo lambda=48.9; -146.3(anti) C3'-endo lambda=60.3 d(C1'-C1')=10.35 d(N1-N9)=8.66 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=-3.7 H-bonds[4]: "N2(amino)-O2(carbonyl)[2.73]; N1(imino)-O2(carbonyl)[2.96]; N1(imino)-N3[2.88]; O6(carbonyl)-N4(amino)[2.91]" bp_pars: [-1.12 -0.48 0.00 -1.14 -4.95 0.91] 10 1:A.U11 1:A.G18 [U-G] Wobble 28-XXVIII cWW cW-W 179.8(anti) C2'-exo lambda=73.0; 179.0(anti) C3'-endo lambda=41.4 d(C1'-C1')=10.43 d(N1-N9)=8.92 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-10.8 H-bonds[2]: "O2(carbonyl)-N1(imino)[2.77]; N3(imino)-O6(carbonyl)[3.10]" bp_pars: [2.87 -0.48 0.31 2.52 -10.16 5.14] 11 1:A.G12 1:A.C17 [G-C] WC 19-XIX cWW cW-W -161.4(anti) C2'-exo lambda=50.6; -165.3(anti) C3'-endo lambda=58.2 d(C1'-C1')=10.43 d(N1-N9)=8.73 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=8.4 H-bonds[3]: "N2(amino)-O2(carbonyl)[2.67]; N1(imino)-N3[2.82]; O6(carbonyl)-N4(amino)[2.88]" bp_pars: [-0.74 -0.38 -0.46 -3.96 6.39 0.45] 12 1:A.G13 1:A.A16 [G-A] 00-n/a tSH tm-M -153.4(anti) C3'-endo lambda=84.3; -123.0(anti) C2'-exo lambda=13.9 d(C1'-C1')=10.17 d(N1-N9)=8.77 d(C6-C8)=8.78 tor(N1-C1'-C1'-N9)=-133.6 H-bonds[3]: "N2(amino)-OP2[2.91]; N2(amino)-N7[2.77]; N1(imino)-OP2[3.36]" bp_pars: [7.44 -4.81 0.91 9.83 -3.85 -34.76] 13 1:A.U22 1:A.A33 [U-A] WC 20-XX cWW cW-W -163.0(anti) C3'-endo lambda=55.5; -156.4(anti) C2'-exo lambda=53.0 d(C1'-C1')=10.41 d(N1-N9)=8.70 d(C6-C8)=9.62 tor(N1-C1'-C1'-N9)=8.9 H-bonds[2]: "N3(imino)-N1[2.68]; O4(carbonyl)-N6(amino)[2.72]" bp_pars: [0.20 -0.34 -0.34 2.11 7.69 -1.64] 14 1:A.G23 1:A.U32 [G-U] 00-n/a cWW cW-W -177.3(anti) C3'-endo lambda=39.7; -160.7(anti) C3'-endo lambda=79.3 d(C1'-C1')=10.13 d(N1-N9)=8.75 d(C6-C8)=9.81 tor(N1-C1'-C1'-N9)=5.1 H-bonds[2]: "N1(imino)-O2(carbonyl)[2.64]; O6(carbonyl)-N3(imino)[3.06]" bp_pars: [-3.38 -0.77 -0.54 -5.70 1.77 8.89] 15 1:A.A24 1:A.U31 [A-U] WC 20-XX cWW cW-W -160.9(anti) C3'-endo lambda=57.0; -162.3(anti) C3'-endo lambda=55.7 d(C1'-C1')=10.28 d(N1-N9)=8.66 d(C6-C8)=9.67 tor(N1-C1'-C1'-N9)=2.4 H-bonds[2]: "N1-N3(imino)[2.64]; N6(amino)-O4(carbonyl)[2.81]" bp_pars: [0.10 -0.28 -0.21 -4.18 1.32 2.45] 16 1:A.C25 1:A.G30 [C-G] WC 19-XIX cWW cW-W -162.2(anti) C3'-endo lambda=61.8; -177.4(anti) C2'-exo lambda=45.0 d(C1'-C1')=10.37 d(N1-N9)=8.65 d(C6-C8)=9.53 tor(N1-C1'-C1'-N9)=4.8 H-bonds[5]: "O2(carbonyl)-N2(amino)[2.99]; O2(carbonyl)-N1(imino)[2.80]; N3-N1(imino)[3.05]; N3*O6(carbonyl)[2.71]; N4(amino)-O6(carbonyl)[3.01]" bp_pars: [1.55 -0.61 -0.37 5.72 2.80 -1.48] 17 1:A.U26 1:A.G29 [U+G] 00-n/a tSW tm+W -148.5(anti) C3'-endo lambda=108.7; 49.1(syn) C3'-endo lambda=16.0 d(C1'-C1')=9.14 d(N1-N9)=8.40 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=-158.2 H-bonds[2]: "O2(carbonyl)-N1(imino)[2.70]; O2'(hydroxyl)-O6(carbonyl)[2.79]" bp_pars: [1.65 -4.54 -0.39 9.70 -8.50 -87.82] **************************************************************************** List of 3 helices helix=1[1] bps=6 1 1:A.G1 1:A.C47 [G-C] WC 19-XIX cWW cW-W 2 1:A.G2 1:A.C46 [G-C] WC 19-XIX cWW cW-W 3 1:A.A3 1:A.U45 [A-U] WC 20-XX cWW cW-W 4 1:A.U4 1:A.A44 [U-A] WC 20-XX cWW cW-W 5 1:A.C5 1:A.G43 [C-G] WC 19-XIX cWW cW-W 6 1:A.A6 1:A.U42 [A-U] WC 20-XX cWW cW-W helix=2[1] bps=6 1 1:A.C7 1:A.A21 [C-A] 00-n/a tHW cM-W 2 1:A.U9 1:A.A20 [U-A] WC 20-XX cWW cW-W 3 1:A.G10 1:A.C19 [G-C] WC 19-XIX cWW cW-W 4 1:A.U11 1:A.G18 [U-G] Wobble 28-XXVIII cWW cW-W 5 1:A.G12 1:A.C17 [G-C] WC 19-XIX cWW cW-W 6 1:A.G13 1:A.A16 [G-A] 00-n/a tSH tm-M helix=3[1] bps=5 1 1:A.U22 1:A.A33 [U-A] WC 20-XX cWW cW-W 2 1:A.G23 1:A.U32 [G-U] 00-n/a cWW cW-W 3 1:A.A24 1:A.U31 [A-U] WC 20-XX cWW cW-W 4 1:A.C25 1:A.G30 [C-G] WC 19-XIX cWW cW-W 5 1:A.U26 1:A.G29 [U+G] 00-n/a tSW tm+W **************************************************************************** List of 3 stems stem=1[#1] bps=6 1 1:A.G1 1:A.C47 [G-C] WC 19-XIX cWW cW-W 2 1:A.G2 1:A.C46 [G-C] WC 19-XIX cWW cW-W 3 1:A.A3 1:A.U45 [A-U] WC 20-XX cWW cW-W 4 1:A.U4 1:A.A44 [U-A] WC 20-XX cWW cW-W 5 1:A.C5 1:A.G43 [C-G] WC 19-XIX cWW cW-W 6 1:A.A6 1:A.U42 [A-U] WC 20-XX cWW cW-W stem=2[#2] bps=4 1 1:A.U9 1:A.A20 [U-A] WC 20-XX cWW cW-W 2 1:A.G10 1:A.C19 [G-C] WC 19-XIX cWW cW-W 3 1:A.U11 1:A.G18 [U-G] Wobble 28-XXVIII cWW cW-W 4 1:A.G12 1:A.C17 [G-C] WC 19-XIX cWW cW-W stem=3[#3] bps=2 1 1:A.A24 1:A.U31 [A-U] WC 20-XX cWW cW-W 2 1:A.C25 1:A.G30 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 1:A.U22 1:A.A33 [U-A] WC 20-XX cWW cW-W **************************************************************************** List of 2 hairpin loop(s) 1 nts=4 GCGA closed by pair {1:A.G12+1:A.C17 [GC], #2} 1:A.G12+1:A.G13+1:A.C14+1:A.G15+1:A.A16+1:A.C17 [GGCGAC] 2 nts=4 UUCG closed by pair {1:A.C25+1:A.G30 [CG], #3} 1:A.C25+1:A.U26+1:A.U27+1:A.C28+1:A.G29+1:A.G30 [CUUCGG] **************************************************************************** List of 1 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#-1, #3] 1:A.U22+1:A.G23+1:A.A24+1:A.U31+1:A.U32+1:A.A33 [UGAUUA] **************************************************************************** List of 1 junction(s) 1 3-way junctions: 17 nts; [2x1x8]; linked by [#1, #2, #-1] 1:A.A6+1:A.C7+1:A.U8+1:A.U9+1:A.A20+1:A.A21+1:A.U22+1:A.A33+1:A.A34+1:A.A35+1:A.A36+1:A.U37+1:A.U38+1:A.C39+1:A.U40+1:A.A41+1:A.U42 [ACUUAAUAAAAUUCUAU] **************************************************************************** >chain-A #1 RNA with 47 nts GGAUCACUUGUGGCGACGCAAUGACUUCGGUUAAAAUUCUAUGAUCC ((((((..((((....)))).(.((....)).)........)))))) DONE!