1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Robinson, 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 C62 H66 N2 O20 2 1159.189 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] WP631 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 US Biochemistry BICHAW 0033 0006-2960 36 8663 8670 10.1021/bi970842j 9289011 Binding of two novel bisdaunorubicins to DNA studied by NMR spectroscopy. 1997 10.2210/pdb1al9/pdb pdb_00001al9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 WP631 IS AN INTERCALATOR 2426.617 DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3') 2 syn polymer 1159.189 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] 1 syn non-polymer no no (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DT) ACGTACGT A,B polydeoxyribonucleotide n n n n n n n n 5.149 1 20 A 1 B 16 8.773 A_DA1:DT16_B 1 3.767 0.255 0.453 -0.022 13.971 1 19 A 2 B 15 -6.375 A_DC2:DG15_B 2 -6.261 0.587 -0.035 -0.276 -18.129 1 19 A 3 B 14 4.370 A_DG3:DC14_B 3 9.481 -0.482 -0.324 -0.124 -6.360 1 20 A 4 B 13 -1.813 A_DT4:DA13_B 4 -11.052 -0.083 0.312 -0.067 6.429 1 20 A 5 B 12 -1.893 A_DA5:DT12_B 5 -11.165 0.086 0.320 -0.074 18.184 1 19 A 6 B 11 4.374 A_DC6:DG11_B 6 9.451 0.483 -0.322 -0.133 -13.983 1 19 A 7 B 10 -6.295 A_DG7:DC10_B 7 -6.332 -0.600 -0.033 -0.286 -5.284 1 20 A 8 B 9 8.955 A_DT8:DA9_B 8 3.881 -0.268 0.459 -0.021 3.031 30.909 A A 1 2 -10.749 B B 16 15 3.105 -5.668 -0.191 -0.320 AA_DA1DC2:DG15DT16_BB 1 5.499 -10.428 29.907 0.448 1.375 6.862 35.666 A A 2 3 -7.724 B B 15 14 6.947 -4.715 1.037 0.611 AA_DC2DG3:DC14DG15_BB 2 2.263 -3.707 35.292 2.448 -0.997 3.105 27.991 A A 3 4 -2.390 B B 14 13 2.980 -1.150 -0.910 -0.367 AA_DG3DT4:DA13DC14_BB 3 -4.904 10.191 27.543 -0.504 0.792 3.600 35.924 A A 4 5 16.783 B B 13 12 3.464 10.217 -0.002 0.979 AA_DT4DA5:DT12DA13_BB 4 -0.103 0.170 34.487 -0.024 -0.013 3.107 28.023 A A 5 6 -2.508 B B 12 11 2.981 -1.208 0.911 -0.368 AA_DA5DC6:DG11DT12_BB 5 4.985 -10.351 27.558 -0.492 -0.775 6.863 35.692 A A 6 7 -7.730 B B 11 10 6.948 -4.722 -1.036 0.611 AA_DC6DG7:DC10DG11_BB 6 -2.267 3.711 35.318 2.448 0.994 3.031 30.966 A A 7 8 -10.588 B B 10 9 3.106 -5.593 0.191 -0.320 AA_DG7DT8:DA9DC10_BB 7 -5.586 10.574 29.964 0.431 -1.388 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1997-09-17 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 _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id MINIMIZED AVERAGE STRUCTURE Y BNL 1997-06-12 REL REL BDA 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] IONIC_STRENGTH: 20 MM PRESSURE: NULL SOLVENT SYSTEM: H2O MINIMIZED AVERAGE 1 1 NOESY TOCSY 7.0 275 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. NOE-RMD BRUNGER refinement X-PLOR structure solution X-PLOR structure solution SPEDREF 750 Varian INOVA 750 DM1 17 2 BDA BDA 17 A A 1 n 1 DA 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A T 4 n 4 DT 4 A A 5 n 5 DA 5 A C 6 n 6 DC 6 A G 7 n 7 DG 7 A T 8 n 8 DT 8 A A 9 n 1 DA 9 B C 10 n 2 DC 10 B G 11 n 3 DG 11 B T 12 n 4 DT 12 B A 13 n 5 DA 13 B C 14 n 6 DC 14 B G 15 n 7 DG 15 B T 16 n 8 DT 16 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 DT 4 0.085 SIDE CHAIN 1 A DC 6 0.092 SIDE CHAIN 1 B DT 12 0.085 SIDE CHAIN 1 B DC 14 0.092 SIDE CHAIN 1 4.48 0.60 106.00 110.48 A A A O4' C4' C3' DA DA DA 1 1 1 N 1 -5.02 0.70 108.00 102.98 A A A O4' C1' N9 DA DA DA 1 1 1 N 1 -5.15 0.80 105.90 100.75 A A A O4' C1' C2' DC DC DC 2 2 2 N 1 4.80 0.30 108.30 113.10 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.63 0.60 106.00 109.63 A A A O4' C4' C3' DG DG DG 3 3 3 N 1 -2.51 0.40 106.40 103.89 A A A C8 N9 C4 DG DG DG 3 3 3 N 1 4.34 0.30 108.30 112.64 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 -4.37 0.70 102.20 97.83 A A A C4' C3' C2' DA DA DA 5 5 5 N 1 2.29 0.30 108.30 110.59 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 5.26 0.60 106.00 111.26 A A A O4' C4' C3' DG DG DG 7 7 7 N 1 -5.25 0.60 122.90 117.65 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 4.52 0.60 106.00 110.52 B B B O4' C4' C3' DA DA DA 9 9 9 N 1 -4.95 0.70 108.00 103.05 B B B O4' C1' N9 DA DA DA 9 9 9 N 1 -5.14 0.80 105.90 100.76 B B B O4' C1' C2' DC DC DC 10 10 10 N 1 4.85 0.30 108.30 113.15 B B B O4' C1' N1 DC DC DC 10 10 10 N 1 3.72 0.60 106.00 109.72 B B B O4' C4' C3' DG DG DG 11 11 11 N 1 -2.48 0.40 106.40 103.92 B B B C8 N9 C4 DG DG DG 11 11 11 N 1 4.09 0.30 108.30 112.39 B B B O4' C1' N1 DT DT DT 12 12 12 N 1 -4.44 0.70 102.20 97.76 B B B C4' C3' C2' DA DA DA 13 13 13 N 1 2.31 0.30 108.30 110.61 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 2.62 0.30 108.30 110.92 B B B O4' C1' N1 DC DC DC 14 14 14 N 1 4.85 0.60 106.00 110.85 B B B O4' C4' C3' DG DG DG 15 15 15 N 1 -3.79 0.60 122.90 119.11 B B B C6 C5 C7 DT DT DT 16 16 16 N 1 B B C5 C7 DT DT 12 12 0.037 0.006 1.496 1.533 N model building X-PLOR refinement X-PLOR phasing X-PLOR NMR STUDY OF DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3') SELF-COMPLEMENTARY DUPLEX COMPLEXED WITH A BIS-DAUNORUBICIN, MINIMIZED AVERAGE STRUCTURE 1 N N 1 N N 2 N N hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 16 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 16 B O4 DT 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 WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 14 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 14 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 14 B N4 DC 6 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 13 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 13 B N6 DA 5 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 12 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 12 B O4 DT 4 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 11 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 11 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 11 B N2 DG 3 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 10 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 10 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 10 B N4 DC 2 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 9 B N1 DA 1 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 9 B N6 DA 1 1_555 DNA COMPLEX (DEOXYRIBONUCLEIC ACID-DRUG), BIS-INTERCALATOR, DAUNORUBICIN, DNA, DEOXYRIBONUCLEIC ACID 1AL9 PDB 1 1AL9 1 8 1AL9 1 8 1AL9 A 1 1 8 9 16 1AL9 9 16 1AL9 B 1 1 8 BINDING SITE FOR RESIDUE BDA A 17 A BDA 17 Software 12 A DC 2 A DC 2 12 1_555 A DG 3 A DG 3 12 1_555 A DT 4 A DT 4 12 1_555 A DA 5 A DA 5 12 1_555 A DC 6 A DC 6 12 1_555 A DG 7 A DG 7 12 1_555 B DC 10 B DC 2 12 1_555 B DG 11 B DG 3 12 1_555 B DT 12 B DT 4 12 1_555 B DA 13 B DA 5 12 1_555 B DC 14 B DC 6 12 1_555 B DG 15 B DG 7 12 1_555 1 P 1