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. Kerwin, S.M. Kenyon, G.L. 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/pdb140d/pdb pdb_0000140d 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 -6.836 1 20 A 1 B 26 -5.661 A_DA1:DT26_B 1 -13.781 0.204 -0.062 -0.100 3.453 1 19 A 2 B 25 0.029 A_DG2:DC25_B 2 -10.858 -0.321 0.451 -0.178 -10.412 1 19 A 3 B 24 -3.284 A_DC3:DG24_B 3 -14.471 0.064 0.343 -0.171 -6.435 1 20 A 4 B 23 0.084 A_DT4:DA23_B 4 -10.834 0.018 0.174 -0.166 8.000 1 20 A 5 B 22 -2.714 A_DT5:DA22_B 5 -3.940 -0.043 0.027 -0.116 9.641 1 19 A 6 B 21 -0.370 A_DG6:DC21_B 6 -13.446 -0.458 0.293 -0.228 -12.606 1 19 A 7 B 20 1.413 A_DC7:DG20_B 7 10.584 0.202 0.658 -0.158 -5.175 1 19 A 8 B 19 -0.358 A_DC8:DG19_B 8 -3.866 0.471 0.440 -0.238 -9.284 1 20 A 9 B 18 -4.437 A_DT9:DA18_B 9 -15.844 -0.227 -0.035 -0.096 1.459 1 20 A 10 B 17 1.478 A_DT10:DA17_B 10 -1.689 -0.054 -0.122 -0.138 2.391 1 19 A 11 B 16 -1.202 A_DG11:DC16_B 11 -9.655 -0.423 -0.322 -0.264 -10.687 1 20 A 12 B 15 3.462 A_DA12:DT15_B 12 -1.074 -0.018 -0.319 -0.109 0.547 1 19 A 13 B 14 -2.556 A_DG13:DC14_B 13 -3.618 -0.278 0.243 -0.203 2.897 31.203 A A 1 2 -8.504 B B 26 25 2.898 -4.554 0.493 -0.551 AA_DA1DG2:DC25DT26_BB 1 -2.580 4.818 30.772 -0.251 -1.355 3.341 38.412 A A 2 3 5.583 B B 25 24 3.448 3.666 0.092 -0.996 AA_DG2DC3:DG24DC25_BB 2 2.344 -3.570 38.174 -1.990 0.164 3.198 34.888 A A 3 4 -1.114 B B 24 23 3.138 -0.666 0.631 -0.504 AA_DC3DT4:DA23DG24_BB 3 4.032 -6.739 34.655 -0.742 -0.458 3.090 32.960 A A 4 5 -3.735 B B 23 22 3.069 -2.117 -0.081 -0.413 AA_DT4DT5:DA22DA23_BB 4 -1.184 2.089 32.873 -0.388 -0.048 2.800 29.803 A A 5 6 11.694 B B 22 21 3.025 5.967 0.205 -0.690 AA_DT5DG6:DC21DA22_BB 5 -2.784 5.455 29.082 -2.464 -0.922 3.236 43.058 A A 6 7 30.954 B B 21 20 4.058 21.751 -0.203 -0.641 AA_DG6DC7:DG20DC21_BB 6 -2.050 2.918 37.332 -3.459 0.033 2.991 34.615 A A 7 8 16.491 B B 20 19 3.162 9.685 0.104 -0.197 AA_DC7DC8:DG19DG20_BB 7 1.639 -2.790 33.233 -1.764 0.068 2.942 35.236 A A 8 9 13.904 B B 19 18 3.120 8.276 0.365 -0.435 AA_DC8DT9:DA18DG19_BB 8 7.740 -13.004 33.419 -1.891 0.492 3.045 37.453 A A 9 10 1.446 B B 18 17 3.006 0.928 1.290 0.190 AA_DT9DT10:DA17DA18_BB 9 1.090 -1.698 37.427 0.184 -1.877 2.541 31.199 A A 10 11 30.607 B B 17 16 3.080 15.733 -0.039 -0.263 AA_DT10DG11:DC16DA17_BB 10 1.487 -2.892 26.987 -3.258 0.334 2.744 33.385 A A 11 12 17.394 B B 16 15 3.356 9.840 -0.369 -1.705 AA_DG11DA12:DT15DC16_BB 11 -2.865 5.065 31.816 -4.529 0.187 2.953 33.982 A A 12 13 -4.209 B B 15 14 2.905 -2.452 -0.166 -0.790 AA_DA12DG13:DC14DT15_BB 12 -3.935 6.754 33.673 -1.000 -0.283 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 2008-03-03 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 (B DNA USED AS STARTING STRUCTURE) MINIMIZED AVERAGE 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 0.086 SIDE CHAIN 1 A DG 6 0.071 SIDE CHAIN 1 A DC 7 0.085 SIDE CHAIN 1 A DG 11 0.067 SIDE CHAIN 1 B DC 16 0.081 SIDE CHAIN 1 B DA 17 0.068 SIDE CHAIN 1 B DA 18 0.063 SIDE CHAIN 1 B DC 21 0.069 SIDE CHAIN 1 B DG 24 0.092 SIDE CHAIN 1 B DC 25 0.068 SIDE CHAIN 1 5.14 0.30 108.30 113.44 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 5.85 0.30 108.30 114.15 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 3.63 0.60 106.00 109.63 A A A O4' C4' C3' DT DT DT 4 4 4 N 1 7.34 1.10 109.80 117.14 A A A C5' C4' O4' DT DT DT 4 4 4 N 1 2.55 0.30 108.30 110.85 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 5.98 0.30 108.30 114.28 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 3.92 0.30 108.30 112.22 A A A O4' C1' N1 DT DT DT 9 9 9 N 1 2.29 0.30 108.30 110.59 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 5.79 0.30 108.30 114.09 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 5.14 0.60 106.00 111.14 A A A O4' C4' C3' DA DA DA 12 12 12 N 1 5.10 0.30 108.30 113.40 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 2.24 0.30 108.30 110.54 B B B O4' C1' N1 DC DC DC 14 14 14 N 1 3.12 0.30 108.30 111.42 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 6.75 0.60 106.00 112.75 B B B O4' C4' C3' DC DC DC 16 16 16 N 1 8.75 1.10 109.80 118.55 B B B C5' C4' O4' DC DC DC 16 16 16 N 1 8.24 1.20 102.50 110.74 B B B C3' C2' C1' DC DC DC 16 16 16 N 1 3.63 0.30 108.30 111.93 B B B O4' C1' N1 DC DC DC 16 16 16 N 1 5.75 0.30 108.30 114.05 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 4.69 0.30 108.30 112.99 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 4.51 0.30 108.30 112.81 B B B O4' C1' N9 DG DG DG 19 19 19 N 1 5.25 0.60 106.00 111.25 B B B O4' C4' C3' DG DG DG 20 20 20 N 1 4.35 0.60 106.00 110.35 B B B O4' C4' C3' DC DC DC 21 21 21 N 1 6.96 1.10 109.80 116.76 B B B C5' C4' O4' DC DC DC 21 21 21 N 1 4.13 0.30 108.30 112.43 B B B O4' C1' N9 DA DA DA 22 22 22 N 1 1.88 0.30 108.30 110.18 B B B O4' C1' N9 DA DA DA 23 23 23 N 1 4.75 0.30 108.30 113.05 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 3.66 0.60 106.00 109.66 B B B O4' C4' C3' DC DC DC 25 25 25 N 1 1.99 0.30 108.30 110.29 B B B O4' C1' N1 DC DC DC 25 25 25 N 1 3.28 0.30 108.30 111.58 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 140D PDB 1 140D 140D PDB 2 140D 1 13 140D 1 13 140D A 1 1 13 14 26 140D 14 26 140D B 2 1 13 1 P 1