1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Marzilli, L.G. Saad, J.S. Kuklenyik, Z. Keating, K.A. Xu, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic Cl2 H6 N2 Pt 300.045 Cisplatin diammine(dichloro)platinum non-polymer 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 N 1 N PT N 2 N N N 3 N N N 4 N H N 5 N H N 6 N H N 7 N H N 8 N CL N 9 N CL N 10 N H N 11 N H N 12 N O N 13 N P N 14 N O N 15 N O N 16 N O N 17 N C N 18 R C N 19 N O N 20 S C N 21 N O N 22 N C N 23 R C Y 24 N N Y 25 N C Y 26 N N Y 27 N C Y 28 N C N 29 N N Y 30 N N Y 31 N C Y 32 N N Y 33 N C N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N O N 49 N P N 50 N O N 51 N O N 52 N O N 53 N C N 54 R C N 55 N O N 56 S C N 57 N O N 58 N C N 59 R C N 60 N N N 61 N C N 62 N O N 63 N N N 64 N C N 65 N N N 66 N C N 67 N C N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N O N 83 N P N 84 N O N 85 N O N 86 N O N 87 N C N 88 R C N 89 N O N 90 S C N 91 N O N 92 N C N 93 R C Y 94 N N Y 95 N C Y 96 N N Y 97 N C N 98 N C N 99 N O N 100 N N N 101 N C N 102 N N N 103 N N Y 104 N C N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N O N 120 N P N 121 N O N 122 N O N 123 N O N 124 N C N 125 R C N 126 N O N 127 S C N 128 N O N 129 N C N 130 R C N 131 N N N 132 N C N 133 N O N 134 N N N 135 N C N 136 N O N 137 N C N 138 N C N 139 N C N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing Y 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing Y 39 N sing Y 40 N doub N 41 N sing Y 42 N doub N 43 N sing N 44 N sing Y 45 N sing Y 46 N doub N 47 N sing Y 48 N sing N 49 N sing N 50 N sing N 51 N doub N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N doub N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing Y 107 N sing Y 108 N sing Y 109 N doub N 110 N sing Y 111 N sing N 112 N sing Y 113 N doub N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N doub N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N doub N 153 N sing N 154 N sing N 155 N doub N 156 N sing N 157 N sing N 158 N sing N 159 N sing US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 2764 2770 10.1021/ja0007915 11456962 Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA. 2001 10.2210/pdb1ksb/pdb pdb_00001ksb 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M x-ray 1 1.0 Cisplatin intrastrand cross-link DNA 2667.749 5'-D(*CP*TP*CP*CP*GP*GP*CP*CP*T)-3' 1 syn polymer 2805.849 5'-D(*AP*GP*GP*CP*CP*GP*GP*AP*G)-3' 1 syn polymer 300.045 Cisplatin 1 syn non-polymer no no (DC)(DT)(DC)(DC)(DG)(DG)(DC)(DC)(DT) CTCCGGCCT A polydeoxyribonucleotide no no (DA)(DG)(DG)(DC)(DC)(DG)(DG)(DA)(DG) AGGCCGGAG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n -4.458 1 19 A 1 B 9 0.471 A_DC1:DG9_B 1 -14.431 -0.119 0.135 0.026 -2.978 1 20 A 2 B 8 -4.302 A_DT2:DA8_B 2 -11.462 -0.549 0.063 -0.075 2.381 1 19 A 3 B 7 2.838 A_DC3:DG7_B 3 -6.238 0.203 -0.195 -0.025 2.568 1 19 A 4 B 6 0.612 A_DC4:DG6_B 4 -0.051 0.451 0.393 -0.126 32.037 1 19 A 5 B 5 -1.719 A_DG5:DC5_B 5 1.835 -0.934 0.579 -0.300 -8.921 1 19 A 6 B 4 -5.597 A_DG6:DC4_B 6 10.165 -0.061 -0.558 -0.258 6.121 1 19 A 7 B 3 -7.634 A_DC7:DG3_B 7 0.358 0.742 0.214 -0.141 13.869 1 19 A 8 B 2 1.530 A_DC8:DG2_B 8 -21.544 0.133 -0.025 -0.005 -4.830 1 20 A 9 B 1 -0.896 A_DT9:DA1_B 9 -15.177 -0.236 -0.015 -0.041 3.104 32.975 A A 1 2 10.749 B B 9 8 3.189 6.068 -0.132 -0.185 AA_DC1DT2:DA8DG9_BB 1 -0.043 0.076 32.427 -1.327 0.226 3.150 38.079 A A 2 3 7.078 B B 8 7 3.128 4.603 0.550 0.089 AA_DT2DC3:DG7DA8_BB 2 3.056 -4.699 37.691 -0.428 -0.469 3.360 34.149 A A 3 4 20.946 B B 7 6 3.359 12.020 -0.495 0.500 AA_DC3DC4:DG6DG7_BB 3 -4.188 7.299 31.754 -1.179 0.136 2.399 28.862 A A 4 5 -22.156 B B 6 5 2.994 -10.656 1.497 1.840 AA_DC4DG5:DC5DG6_BB 4 7.599 -15.801 25.780 5.764 -1.526 0.915 65.829 A A 5 6 76.687 B B 5 4 5.591 63.763 -0.224 -0.622 AA_DG5DG6:DC4DC5_BB 5 -4.064 4.888 16.764 -5.111 -0.083 3.246 38.789 A A 6 7 5.264 B B 4 3 3.177 3.469 -0.761 -0.080 AA_DG6DC7:DG3DC4_BB 6 -7.853 11.916 37.863 -0.543 0.192 2.639 31.854 A A 7 8 20.453 B B 3 2 2.967 10.948 0.988 -0.829 AA_DC7DC8:DG2DG3_BB 7 5.568 -10.401 29.447 -3.292 -0.893 3.416 36.531 A A 8 9 15.884 B B 2 1 3.634 9.829 0.032 -0.311 AA_DC8DT9:DA1DG2_BB 8 3.239 -5.235 35.082 -1.991 0.441 chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software struct_conn struct_site repository Initial release Version format compliance Non-polymer description Version format compliance Data collection Database references Derived calculations 1 0 2002-01-17 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-05-01 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Crystal Structure Of HMG1 Domain A Bound To A Cisplatin-Modified DNA Duplex NMR Solution Structure Of a DNA Dodecamer Duplex Containing a Cis-Diammineplatinum(II) d(GpG) Intrastrand Cross-Link, the Major Adduct Of the Anticancer Drug Cisplatin RCSB Y RCSB 2002-01-11 REL CPT Cisplatin 2D 1H-31P phase-sensitive Reverse Chemical Shift Correlation (RCSC) and 1H-13C magnitude mode HMQC experiments were performed. 1 2D NOESY DQF-COSY 7.0 1 atm 278 K NOE-Restrained refinement (details can be found in the paper) AMBER Platinated 9-mer duplex dissolved in D2O/H2O D2O or (90% H2O, 10% D2O) processing Felix 97.0 Biosym/MSI refinement Discover structure solution Insight II data analysis Curves Biosym/MSI refinement IRMA 600 GE OMEGA 600 Varian UNITYPLUS PT 4 3 CPT CPT 10 A C 1 n 1 DC 1 A T 2 n 2 DT 2 A C 3 n 3 DC 3 A C 4 n 4 DC 4 A G 5 n 5 DG 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A C 8 n 8 DC 8 A T3' 9 n 9 DT 9 A A 1 n 1 DA 1 B G 2 n 2 DG 2 B G 3 n 3 DG 3 B C 4 n 4 DC 4 B C 5 n 5 DC 5 B G 6 n 6 DG 6 B G 7 n 7 DG 7 B A 8 n 8 DA 8 B G3' 9 n 9 DG 9 B author_defined_assembly 2 dimeric A DG 5 A N7 DG 5 1_555 A CPT 10 C PT1 CPT 1_555 A CPT 10 C N1 CPT 1_555 178.5 A DG 5 A N7 DG 5 1_555 A CPT 10 C PT1 CPT 1_555 A CPT 10 C N2 CPT 1_555 90.4 A CPT 10 C N1 CPT 1_555 A CPT 10 C PT1 CPT 1_555 A CPT 10 C N2 CPT 1_555 90.4 A DG 5 A N7 DG 5 1_555 A CPT 10 C PT1 CPT 1_555 A DG 6 A N7 DG 6 1_555 88.6 A CPT 10 C N1 CPT 1_555 A CPT 10 C PT1 CPT 1_555 A DG 6 A N7 DG 6 1_555 90.5 A CPT 10 C N2 CPT 1_555 A CPT 10 C PT1 CPT 1_555 A DG 6 A N7 DG 6 1_555 178.2 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 1 0.069 SIDE CHAIN 1 B DG 2 0.107 SIDE CHAIN 1 B DG 3 0.109 SIDE CHAIN 1 B DC 4 0.086 SIDE CHAIN 1 B DG 6 0.068 SIDE CHAIN 1 3.00 0.30 108.30 111.30 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.77 0.60 106.00 109.77 A A A O4' C4' C3' DT DT DT 2 2 2 N 1 -4.56 0.70 108.00 103.44 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 6.52 0.50 106.80 113.32 A A A O4' C1' C2' DG DG DG 5 5 5 N 1 3.59 0.30 108.30 111.89 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 3.95 0.60 106.00 109.95 B B B O4' C4' C3' DG DG DG 2 2 2 N 1 7.42 0.30 108.30 115.72 B B B O4' C1' N9 DG DG DG 2 2 2 N 1 4.11 0.60 106.00 110.11 B B B O4' C4' C3' DG DG DG 3 3 3 N 1 9.47 1.20 102.50 111.97 B B B C3' C2' C1' DG DG DG 3 3 3 N 1 6.89 0.30 108.30 115.19 B B B O4' C1' N9 DG DG DG 3 3 3 N 1 -3.22 0.50 128.60 125.38 B B B N3 C4 C5 DG DG DG 3 3 3 N 1 3.26 0.50 106.80 110.06 B B B O4' C1' C2' DC DC DC 5 5 5 N 1 3.88 0.60 106.00 109.88 B B B O4' C4' C3' DA DA DA 8 8 8 N 1 1.84 0.30 108.30 110.14 B B B O4' C1' N9 DA DA DA 8 8 8 N 1 2.32 0.30 108.30 110.62 B B B O4' C1' N9 DG DG DG 9 9 9 N 1 B B C5' C4' DC DC 4 4 0.046 0.007 1.512 1.558 N 1 B B O3' C3' DC DC 4 4 -0.110 0.006 1.419 1.309 N 1 B B O3' C3' DC DC 5 5 -0.050 0.006 1.419 1.369 N Relationship of Solution and Protein-Bound Structures of DNA Duplexes with the Major Intrastrand Cross-Link Lesions Formed on Cisplatin Binding to DNA 1 N N 2 N N 3 N N metalc 2.007 A DG 5 A N7 DG 5 1_555 A CPT 10 C PT1 CPT 1_555 metalc 2.012 A DG 6 A N7 DG 6 1_555 A CPT 10 C PT1 CPT 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 9 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 9 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 9 B N2 DG 9 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 8 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 8 B N6 DA 8 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 7 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 7 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 7 B N2 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 6 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 6 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 6 B N2 DG 6 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 5 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 5 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 5 B N4 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 4 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 4 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 4 B N4 DC 4 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 3 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 3 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 3 B N2 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 1 B N1 DA 1 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 1 B N6 DA 1 1_555 DNA Deoxyribonucleic acid, Cisplatin, DNA, Duplex, 9-mer, Intrastrand cross-link, model J 1KSB PDB 1 1KSB 1KSB PDB 2 1KSB 1 9 1KSB 1 9 1KSB A 1 1 9 1 9 1KSB 1 9 1KSB B 2 1 9 BINDING SITE FOR RESIDUE CPT A 10 A CPT 10 Software 2 A DG 5 A DG 5 2 1_555 A DG 6 A DG 6 2 1_555