1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Mujeeb, A. James, T.L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking US Biochemistry BICHAW 0033 0006-2960 32 13419 13431 10.1021/bi00212a007 8257678 Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra. 1993 10.2210/pdb142d/pdb pdb_0000142d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3982.596 DNA (5'-D(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3') 1 syn polymer 3960.600 DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3') 1 syn polymer no no (DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC)(DT)(DT)(DG)(DA)(DG) AGCTTGCCTTGAG A polydeoxyribonucleotide no no (DC)(DT)(DC)(DA)(DA)(DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT) CTCAAGGCAAGCT B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n 0.458 1 20 A 1 B 26 -5.733 A_DA1:DT26_B 1 -13.829 0.185 0.055 -0.130 9.124 1 19 A 2 B 25 0.233 A_DG2:DC25_B 2 -11.062 -0.301 0.502 -0.179 -4.679 1 19 A 3 B 24 -2.208 A_DC3:DG24_B 3 -15.550 0.131 0.165 -0.188 -3.282 1 20 A 4 B 23 1.079 A_DT4:DA23_B 4 -11.835 -0.009 0.046 -0.164 8.481 1 20 A 5 B 22 -1.908 A_DT5:DA22_B 5 -6.334 -0.058 -0.045 -0.127 8.124 1 19 A 6 B 21 0.081 A_DG6:DC21_B 6 -12.721 -0.434 0.238 -0.216 -8.121 1 19 A 7 B 20 0.193 A_DC7:DG20_B 7 1.347 0.240 0.411 -0.155 -0.837 1 19 A 8 B 19 -0.846 A_DC8:DG19_B 8 -6.833 0.359 0.214 -0.216 -4.495 1 20 A 9 B 18 -2.945 A_DT9:DA18_B 9 -16.172 0.047 -0.127 -0.184 3.973 1 20 A 10 B 17 -1.003 A_DT10:DA17_B 10 -10.099 0.067 -0.048 -0.148 -4.554 1 19 A 11 B 16 -1.313 A_DG11:DC16_B 11 -17.630 -0.367 -0.345 -0.263 -15.929 1 20 A 12 B 15 2.463 A_DA12:DT15_B 12 -3.859 -0.017 -0.198 -0.119 -7.194 1 19 A 13 B 14 -3.022 A_DG13:DC14_B 13 -11.442 -0.246 0.297 -0.231 2.999 31.985 A A 1 2 -9.068 B B 26 25 3.002 -4.973 0.578 -0.519 AA_DA1DG2:DC25DT26_BB 1 -2.269 4.137 31.526 -0.111 -1.428 3.366 39.338 A A 2 3 5.653 B B 25 24 3.471 3.794 0.063 -0.863 AA_DG2DC3:DG24DC25_BB 2 4.009 -5.974 38.964 -1.754 0.406 3.274 35.040 A A 3 4 -1.962 B B 24 23 3.230 -1.180 0.526 -0.335 AA_DC3DT4:DA23DG24_BB 3 3.317 -5.518 34.868 -0.380 -0.377 3.136 33.634 A A 4 5 -5.321 B B 23 22 3.116 -3.072 -0.022 -0.422 AA_DT4DT5:DA22DA23_BB 4 -2.369 4.103 33.416 -0.248 -0.334 2.809 30.590 A A 5 6 11.785 B B 22 21 3.055 6.159 0.128 -0.728 AA_DT5DG6:DC21DA22_BB 5 -4.064 7.776 29.708 -2.489 -0.975 3.135 41.062 A A 6 7 23.782 B B 21 20 3.674 16.254 -0.413 -0.727 AA_DG6DC7:DG20DC21_BB 6 -2.156 3.154 37.777 -2.961 0.334 2.845 33.259 A A 7 8 16.227 B B 20 19 3.064 9.173 0.052 -0.400 AA_DC7DC8:DG19DG20_BB 7 0.909 -1.608 31.991 -2.111 0.048 3.000 36.419 A A 8 9 13.233 B B 19 18 3.133 8.161 0.404 -0.364 AA_DC8DT9:DA18DG19_BB 8 6.581 -10.671 34.926 -1.670 0.229 2.909 33.353 A A 9 10 7.302 B B 18 17 3.019 4.180 0.514 -0.572 AA_DT9DT10:DA17DA18_BB 9 -1.102 1.926 33.080 -1.628 -1.062 2.788 35.084 A A 10 11 30.412 B B 17 16 3.261 17.517 0.334 -0.150 AA_DT10DG11:DC16DA17_BB 10 3.752 -6.514 30.290 -2.869 0.007 2.963 34.356 A A 11 12 13.215 B B 16 15 3.317 7.732 -0.305 -1.312 AA_DG11DA12:DT15DC16_BB 11 -3.128 5.346 33.358 -3.401 0.039 3.056 35.026 A A 12 13 -3.627 B B 15 14 3.028 -2.178 -0.131 -0.589 AA_DA12DG13:DC14DT15_BB 12 -3.641 6.063 34.776 -0.673 -0.293 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1994-04-30 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site 1 STRUCTURE (A DNA USED AS STARTING STRUCTURE) 1 STRUCTURE (B DNA USED AS STARTING STRUCTURE) Y BNL 1993-09-24 REL CHEMICALLY SYNTHESIZED sample CHEMICALLY SYNTHESIZED sample SUGAR PUCKER OF DEOXYRIBOSES HAS BEEN DETERMINED BY SIMULATION OF 2QF-COSY SPECTRA. A LIST OF TORSION ANGLE AND NOE DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRY R140DMR. 1 ALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED THREE COORDINATE SETS FOR THIS STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN DATA BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA AND B-DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE AUTHORS DENOTED THESE STRUCTURES AS RMD-A AND RMD-B, RESPECTIVELY. THE THIRD COORDINATE SET (PROTEIN DATA BANK ENTRY 142D) REPRESENTS THE FINAL STRUCTURE, DENOTED RMD-FINAL BY THE AUTHORS. ALL STRUCTURES WERE DERIVED BY AVERAGING THE LAST 4 PS OF 30 PS RESTRAINED MD (AMBER4) AND SUBSEQUENT RESTRAINED ENERGY MINIMIZATION. FIVE RMD RUNS WERE AVERAGED TO EACH INTERIM STRUCTURE RMD-A AND RMD-B, DEPENDING ON THE STARTING GEOMETRY. ALL TEN STRUCTURES WERE AVERAGED, RESTRAINED ENERGY MINIMIZED AND A FINAL 20PS RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, AFTER AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE FINAL STRUCTURE: RMD-FINAL. MOLECULAR DYNAMICS, ENERGY MINIMIZATION structure solution AMBER4 refinement AMBER4 A 1 n 1 DA 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A T 4 n 4 DT 4 A T 5 n 5 DT 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A C 8 n 8 DC 8 A T 9 n 9 DT 9 A T 10 n 10 DT 10 A G 11 n 11 DG 11 A A 12 n 12 DA 12 A G 13 n 13 DG 13 A C 14 n 1 DC 14 B T 15 n 2 DT 15 B C 16 n 3 DC 16 B A 17 n 4 DA 17 B A 18 n 5 DA 18 B G 19 n 6 DG 19 B G 20 n 7 DG 20 B C 21 n 8 DC 21 B A 22 n 9 DA 22 B A 23 n 10 DA 23 B G 24 n 11 DG 24 B C 25 n 12 DC 25 B T 26 n 13 DT 26 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DC 3 0.108 SIDE CHAIN 1 A DT 4 0.073 SIDE CHAIN 1 A DG 6 0.115 SIDE CHAIN 1 B DC 16 0.104 SIDE CHAIN 1 B DG 24 0.092 SIDE CHAIN 1 B DC 25 0.076 SIDE CHAIN 1 4.52 0.30 108.30 112.82 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 5.28 0.30 108.30 113.58 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 3.95 0.60 106.00 109.95 A A A O4' C4' C3' DT DT DT 4 4 4 N 1 7.37 1.10 109.80 117.17 A A A C5' C4' O4' DT DT DT 4 4 4 N 1 2.13 0.30 108.30 110.43 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 4.21 0.60 106.00 110.21 A A A O4' C4' C3' DT DT DT 5 5 5 N 1 5.86 0.30 108.30 114.16 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 2.42 0.30 108.30 110.72 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 3.59 0.30 108.30 111.89 A A A O4' C1' N1 DT DT DT 9 9 9 N 1 2.82 0.30 108.30 111.12 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 5.67 0.30 108.30 113.97 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 5.23 0.60 106.00 111.23 A A A O4' C4' C3' DA DA DA 12 12 12 N 1 5.06 0.30 108.30 113.36 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 1.92 0.30 108.30 110.22 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 6.64 0.60 106.00 112.64 B B B O4' C4' C3' DC DC DC 16 16 16 N 1 7.94 1.10 109.80 117.74 B B B C5' C4' O4' DC DC DC 16 16 16 N 1 9.09 1.20 102.50 111.59 B B B C3' C2' C1' DC DC DC 16 16 16 N 1 3.90 0.30 108.30 112.20 B B B O4' C1' N1 DC DC DC 16 16 16 N 1 4.47 0.30 108.30 112.77 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 3.72 0.60 106.00 109.72 B B B O4' C4' C3' DA DA DA 18 18 18 N 1 5.58 0.30 108.30 113.88 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 3.72 0.60 106.00 109.72 B B B O4' C4' C3' DG DG DG 19 19 19 N 1 4.68 0.30 108.30 112.98 B B B O4' C1' N9 DG DG DG 19 19 19 N 1 5.60 0.60 106.00 111.60 B B B O4' C4' C3' DG DG DG 20 20 20 N 1 6.77 1.10 109.80 116.57 B B B C5' C4' O4' DG DG DG 20 20 20 N 1 4.41 0.60 106.00 110.41 B B B O4' C4' C3' DC DC DC 21 21 21 N 1 7.16 1.10 109.80 116.96 B B B C5' C4' O4' DC DC DC 21 21 21 N 1 3.98 0.30 108.30 112.28 B B B O4' C1' N9 DA DA DA 22 22 22 N 1 4.78 0.30 108.30 113.08 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 3.77 0.60 106.00 109.77 B B B O4' C4' C3' DC DC DC 25 25 25 N 1 2.42 0.30 108.30 110.72 B B B O4' C1' N1 DC DC DC 25 25 25 N 1 2.76 0.30 108.30 111.06 B B B O4' C1' N1 DT DT DT 26 26 26 N refinement AMBER SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA 1 N N 2 N N hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 26 B N3 DT 13 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 26 B O4 DT 13 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 25 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 25 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 25 B N4 DC 12 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 24 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 24 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 24 B N2 DG 11 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 23 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 23 B N6 DA 10 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 22 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 22 B N6 DA 9 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 21 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 21 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 21 B N4 DC 8 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 20 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 20 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 20 B N2 DG 7 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 19 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 19 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 19 B N2 DG 6 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 18 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 18 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 17 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 17 B N6 DA 4 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 16 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 16 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 16 B N4 DC 3 1_555 hydrog WATSON-CRICK A DA 12 A N1 DA 12 1_555 B DT 15 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 12 A N6 DA 12 1_555 B DT 15 B O4 DT 2 1_555 hydrog WATSON-CRICK A DG 13 A N1 DG 13 1_555 B DC 14 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 13 A N2 DG 13 1_555 B DC 14 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 13 A O6 DG 13 1_555 B DC 14 B N4 DC 1 1_555 DNA DNA, DOUBLE HELIX, CONSERVED SEQUENCE OF HIV-1 GENOME 142D PDB 1 142D 142D PDB 2 142D 1 13 142D 1 13 142D A 1 1 13 14 26 142D 14 26 142D B 2 1 13 1 P 1