1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yang, D. Van Boom, S.S.G.E. Reedijk, J. Van Boom, J.H. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 Biochemistry BICHAW 0033 0006-2960 34 12912 12920 10.1021/bi00039a054 7548048 Structure and isomerization of an intrastrand cisplatin-cross-linked octamer DNA duplex by NMR analysis. 1995 UK Prog.Biophys.Mol.Biol. PBIMAC 0918 0079-6107 66 81 Structural Studies of Interactions between Anticancer Platinum Drugs and DNA 1996 Urbana : University of Illinois at Urbana-Champaign (Thesis) US Thesis 2157 1996 10.2210/pdb1au5/pdb pdb_00001au5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 INTRASTRAND CISPLATIN-CROSSLINKED DNA 2378.567 DNA (5'-D(*CP*CP*TP*GP*GP*TP*CP*C)-3') 1 syn polymer INTRASTRAND CISPLATIN-CROSSLINKED DNA 2476.643 DNA (5'-D(*GP*GP*AP*CP*CP*AP*GP*G)-3') 1 syn polymer 300.045 Cisplatin 1 syn non-polymer no no (DC)(DC)(DT)(DG)(DG)(DT)(DC)(DC) CCTGGTCC A polydeoxyribonucleotide no no (DG)(DG)(DA)(DC)(DC)(DA)(DG)(DG) GGACCAGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n 10.237 1 19 A 1 B 16 1.904 A_DC1:DG16_B 1 11.931 -0.157 -0.049 0.026 8.264 1 19 A 2 B 15 -6.400 A_DC2:DG15_B 2 -31.255 1.176 0.292 -0.650 -21.398 1 A 3 B 14 8.696 A_DT3:DA14_B 3 -25.584 0.039 1.011 -0.003 -12.524 1 19 A 4 B 13 6.001 A_DG4:DC13_B 4 -39.686 -0.479 -0.560 -0.422 -16.637 1 19 A 5 B 12 -3.720 A_DG5:DC12_B 5 1.474 -0.880 0.262 -0.356 -0.196 1 20 A 6 B 11 14.785 A_DT6:DA11_B 6 -3.572 0.293 0.333 -0.002 6.449 1 19 A 7 B 10 7.067 A_DC7:DG10_B 7 -16.777 0.651 -0.529 -0.225 -8.387 1 19 A 8 B 9 7.272 A_DC8:DG9_B 8 12.614 0.828 0.082 0.046 3.099 54.719 A A 1 2 -42.892 B B 16 15 4.074 -36.439 -0.292 0.039 AA_DC1DC2:DG15DG16_BB 1 2.680 -3.154 41.453 2.847 0.524 3.927 35.198 A A 2 3 1.229 B B 15 14 3.933 0.741 0.452 -1.475 AA_DC2DT3:DA14DG15_BB 2 4.843 -8.033 34.866 -2.572 0.123 3.024 31.341 A A 3 4 7.536 B B 14 13 3.269 4.005 -0.684 0.859 AA_DT3DG4:DC13DA14_BB 3 9.052 -17.034 29.774 0.845 2.951 1.148 47.658 A A 4 5 61.927 B B 13 12 3.721 41.033 0.993 -0.369 AA_DG4DG5:DC12DC13_BB 4 -12.224 18.448 21.442 -3.967 -2.274 2.657 30.352 A A 5 6 4.559 B B 12 11 2.729 2.380 0.170 -0.874 AA_DG5DT6:DA11DC12_BB 5 3.297 -6.315 30.085 -2.065 0.223 2.801 45.096 A A 6 7 -20.262 B B 11 10 3.040 -15.134 0.047 0.032 AA_DT6DC7:DG10DA11_BB 6 10.296 -13.785 41.392 1.313 0.804 3.904 36.543 A A 7 8 -8.867 B B 10 9 3.877 -5.488 0.238 -1.593 AA_DC7DC8:DG9DG10_BB 7 -8.801 14.218 35.089 -1.620 -1.856 chem_comp_atom chem_comp_bond database_2 pdbx_database_status struct_conn struct_site repository Initial release Version format compliance Non-polymer description Version format compliance Data collection Database references Derived calculations Other 1 0 1998-02-25 1 1 2008-03-24 1 2 2011-07-13 1 3 2024-04-10 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _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 Y BNL 1997-09-11 REL REL CPT Cisplatin 1 1 2D1HNOESY TOCSY 150 mM NACL 7 1 ATM SOLVENT SYSTEM : H2O/D2O 275 K NOE-RESTRAINED REFINEMENT SPEDREF BRUNGER refinement X-PLOR structure solution X-PLOR structure solution QUANTA 500 Varian VXR500 CPT 17 3 CPT CPT 17 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A T 3 n 3 DT 3 A G 4 n 4 DG 4 A G 5 n 5 DG 5 A T 6 n 6 DT 6 A C 7 n 7 DC 7 A C 8 n 8 DC 8 A G 9 n 1 DG 9 B G 10 n 2 DG 10 B A 11 n 3 DA 11 B C 12 n 4 DC 12 B C 13 n 5 DC 13 B A 14 n 6 DA 14 B G 15 n 7 DG 15 B G 16 n 8 DG 16 B author_defined_assembly 2 dimeric A DG 4 A N7 DG 4 1_555 A CPT 17 C PT1 CPT 1_555 A CPT 17 C N1 CPT 1_555 91.2 A DG 4 A N7 DG 4 1_555 A CPT 17 C PT1 CPT 1_555 A CPT 17 C N2 CPT 1_555 177.6 A CPT 17 C N1 CPT 1_555 A CPT 17 C PT1 CPT 1_555 A CPT 17 C N2 CPT 1_555 91.2 A DG 4 A N7 DG 4 1_555 A CPT 17 C PT1 CPT 1_555 A DG 5 A N7 DG 5 1_555 87.4 A CPT 17 C N1 CPT 1_555 A CPT 17 C PT1 CPT 1_555 A DG 5 A N7 DG 5 1_555 178.5 A CPT 17 C N2 CPT 1_555 A CPT 17 C PT1 CPT 1_555 A DG 5 A N7 DG 5 1_555 90.2 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 B DA 11 0.082 SIDE CHAIN 1 -4.51 0.70 102.20 97.69 A A A C4' C3' C2' DC DC DC 1 1 1 N 1 5.02 0.30 108.30 113.32 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 6.50 0.30 108.30 114.80 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.46 0.30 108.30 111.76 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 8.29 1.20 119.70 127.99 A A A C3' O3' P DT DT DG 3 3 4 Y 1 -4.22 0.70 102.20 97.98 A A A C4' C3' C2' DG DG DG 4 4 4 N 1 8.52 0.30 108.30 116.82 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -5.04 0.80 105.90 100.86 A A A O4' C1' C2' DG DG DG 5 5 5 N 1 7.54 0.30 108.30 115.84 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 5.30 0.30 108.30 113.60 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 6.71 0.30 108.30 115.01 B B B O4' C1' N9 DG DG DG 9 9 9 N 1 2.39 0.30 108.30 110.69 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 12.57 0.30 108.30 120.87 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 4.31 0.60 118.90 123.21 B B B N1 C2 O2 DC DC DC 12 12 12 N 1 7.52 1.10 109.80 117.32 B B B C5' C4' O4' DC DC DC 13 13 13 N 1 -6.09 0.80 105.90 99.81 B B B O4' C1' C2' DA DA DA 14 14 14 N 1 3.25 0.30 108.30 111.56 B B B O4' C1' N9 DA DA DA 14 14 14 N 1 2.85 0.30 108.30 111.15 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 -5.25 0.80 105.90 100.65 B B B O4' C1' C2' DG DG DG 16 16 16 N 1 10.59 0.30 108.30 118.89 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 A A C5' C4' DT DT 3 3 0.058 0.007 1.512 1.570 N 1 A A C5 C7 DT DT 3 3 0.066 0.006 1.496 1.562 N 1 A A C5 C7 DT DT 6 6 0.061 0.006 1.496 1.557 N model building X-PLOR refinement X-PLOR phasing X-PLOR SOLUTION STRUCTURE OF INTRASTRAND CISPLATIN-CROSSLINKED DNA OCTAMER D(CCTG*G*TCC):D(GGACCAGG), NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N 3 N N metalc 1.984 A DG 4 A N7 DG 4 1_555 A CPT 17 C PT1 CPT 1_555 metalc 1.963 A DG 5 A N7 DG 5 1_555 A CPT 17 C PT1 CPT 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 16 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 16 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 16 B N2 DG 8 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 15 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 15 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 15 B N2 DG 7 1_555 hydrog DT-DA PAIR A DT 3 A N3 DT 3 1_555 B DA 14 B N1 DA 6 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 13 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 13 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 13 B N4 DC 5 1_555 hydrog DG-DA MISPAIR A DG 5 A O6 DG 5 1_555 B DA 11 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 12 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 12 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 12 B N4 DC 4 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 11 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 11 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 10 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 10 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 10 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 9 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 9 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 9 B N2 DG 1 1_555 DNA INTRASTRAND, CISPLATIN, DNA, DEOXYRIBONUCLEIC ACID 1AU5 PDB 1 1AU5 1AU5 PDB 2 1AU5 1 8 1AU5 1 8 1AU5 A 1 1 8 9 16 1AU5 9 16 1AU5 B 2 1 8 BINDING SITE FOR RESIDUE CPT A 17 A CPT 17 Software 3 A DG 4 A DG 4 3 1_555 A DG 5 A DG 5 3 1_555 A DT 6 A DT 6 3 1_555 1 P 1