0.035373 0.000000 0.000000 0.000000 0.035373 0.000000 0.000000 0.000000 0.018598 0.00000 0.00000 0.00000 Hu, G.G. Shui, X. Leng, F. Priebe, W. Chaires, J.B. Williams, L.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 28.270 28.270 53.770 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 H2 O 18.015 WATER non-polymer Y 1 N C Y 2 N C Y 3 N C Y 4 N C N 5 N O Y 6 N C N 7 N C N 8 N O Y 9 N C Y 10 N C N 11 N O Y 12 N C N 13 S C N 14 N O N 15 N C N 16 S C N 17 N O N 18 N C N 19 N O N 20 N C N 21 N C Y 22 N C Y 23 N C N 24 N O Y 25 N C N 26 N C N 27 N O Y 28 N C N 29 N C N 30 R C N 31 N C N 32 S C N 33 N N N 34 S C N 35 N O N 36 S C N 37 N O N 38 N C N 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C Y 44 N C Y 45 N C Y 46 N C N 47 N O Y 48 N C N 49 N C N 50 N O Y 51 N C Y 52 N C N 53 N O Y 54 N C N 55 S C N 56 N O N 57 N C N 58 S C N 59 N O N 60 N C N 61 N O N 62 N C N 63 N C Y 64 N C Y 65 N C N 66 N O Y 67 N C N 68 N C N 69 N O Y 70 N C N 71 N C N 72 R C N 73 N C N 74 S C N 75 N N N 76 S C N 77 N O N 78 S C N 79 N O N 80 N C N 81 N C Y 82 N C Y 83 N C Y 84 N C N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H 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 H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H 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 O N 152 N P N 153 N O N 154 N O N 155 N O N 156 N C N 157 R C N 158 N O N 159 S C N 160 N O N 161 N C N 162 R C Y 163 N N Y 164 N C Y 165 N N Y 166 N C Y 167 N C N 168 N N Y 169 N N Y 170 N C Y 171 N N Y 172 N C N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N O N 188 N P N 189 N O N 190 N O N 191 N O N 192 N C N 193 R C N 194 N O N 195 S C N 196 N O N 197 N C N 198 R C N 199 N N N 200 N C N 201 N O N 202 N N N 203 N C N 204 N N N 205 N C N 206 N C N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N O N 222 N P N 223 N O N 224 N O N 225 N O N 226 N C N 227 R C N 228 N O N 229 S C N 230 N O N 231 N C N 232 R C Y 233 N N Y 234 N C Y 235 N N Y 236 N C N 237 N C N 238 N O N 239 N N N 240 N C N 241 N N N 242 N N Y 243 N C N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N O N 259 N P N 260 N O N 261 N O N 262 N O N 263 N C N 264 R C N 265 N O N 266 S C N 267 N O N 268 N C N 269 R C N 270 N N N 271 N C N 272 N O N 273 N N N 274 N C N 275 N O N 276 N C N 277 N C N 278 N C N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N O N 295 N H N 296 N H Y 1 N doub Y 2 N sing N 3 N sing Y 4 N sing N 5 N sing Y 6 N doub N 7 N sing N 8 N sing Y 9 N sing N 10 N sing N 11 N sing Y 12 N doub N 13 N doub N 14 N sing Y 15 N sing Y 16 N doub N 17 N sing Y 18 N doub N 19 N sing N 20 N sing Y 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 doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing Y 41 N doub N 42 N sing Y 43 N sing N 44 N sing N 45 N sing N 46 N doub N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing 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 sing N 75 N sing Y 76 N doub Y 77 N sing Y 78 N sing N 79 N sing Y 80 N doub N 81 N sing Y 82 N doub Y 83 N sing N 84 N sing Y 85 N sing N 86 N sing Y 87 N doub N 88 N sing N 89 N sing Y 90 N sing N 91 N sing N 92 N sing Y 93 N doub N 94 N doub N 95 N sing Y 96 N sing Y 97 N doub N 98 N sing Y 99 N doub N 100 N sing N 101 N sing Y 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing Y 122 N doub N 123 N sing Y 124 N sing N 125 N sing N 126 N sing N 127 N doub 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 sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing Y 157 N doub Y 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N doub N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing Y 184 N sing Y 185 N sing Y 186 N doub N 187 N sing Y 188 N sing Y 189 N sing Y 190 N doub N 191 N sing Y 192 N doub N 193 N sing N 194 N sing Y 195 N sing Y 196 N doub N 197 N sing Y 198 N sing N 199 N sing N 200 N sing N 201 N doub N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N doub N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N doub N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N doub N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing Y 257 N sing Y 258 N sing Y 259 N doub N 260 N sing Y 261 N sing N 262 N sing Y 263 N doub N 264 N doub N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N doub N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N doub N 299 N sing N 300 N sing N 301 N sing N 302 N doub N 303 N sing N 304 N sing N 305 N doub N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing US Biochemistry BICHAW 0033 0006-2960 36 5940 5946 10.1021/bi9705218 9166763 Structure of a DNA-bisdaunomycin complex. 1997 10.2210/pdb1agl/pdb pdb_00001agl 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 294.00 1 AREA DETECTOR 1996-05-01 SDMS GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.0 ROTATING ANODE RIGAKU RU200 1809.217 DNA (5'-D(*CP*GP*AP*TP*CP*G)-3') 1 syn polymer 1159.189 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] 1 syn non-polymer 18.015 water 8 nat water no no (DC)(DG)(DA)(DT)(DC)(DG) CGATCG A polydeoxyribonucleotide n n n n n n 1 2.84 56.74 VAPOR DIFFUSION, SITTING DROP 6.50 pH 6.50, VAPOR DIFFUSION, SITTING DROP ROOM TEMPERATURE WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE_HCL 1 WATER 2 MPD 2 7.237 1 19 A 1 A 6 -0.918 A_DC1:DG6_A 1 1.710 0.410 -0.099 -0.367 -20.524 1 19 A 2 A 5 -0.778 A_DG2:DC5_A 2 2.722 -0.610 -0.312 -0.530 -2.211 1 20 A 3 A 4 4.199 A_DA3:DT4_A 3 -5.817 -0.184 0.214 -0.211 2.211 1 20 A 4 A 3 4.199 A_DT4:DA3_A 4 -5.817 0.184 0.214 -0.211 20.524 1 19 A 5 A 2 -0.778 A_DC5:DG2_A 5 2.722 0.610 -0.312 -0.530 -7.237 1 19 A 6 A 1 -0.918 A_DG6:DC1_A 6 1.709 -0.410 -0.099 -0.367 7.190 31.554 A A 1 2 -1.909 A A 6 5 7.184 -1.036 0.884 1.325 AA_DC1DG2:DC5DG6_AA 1 3.211 -5.916 31.378 2.860 -0.312 3.254 36.213 A A 2 3 4.661 A A 5 4 3.036 2.873 -0.777 1.720 AA_DG2DA3:DT4DC5_AA 2 -7.839 12.719 35.269 2.373 0.176 3.413 29.976 A A 3 4 -3.724 A A 4 3 3.382 -1.925 0.000 -0.596 AA_DA3DT4:DA3DT4_AA 3 0.000 0.000 29.915 -0.741 0.000 3.254 36.213 A A 4 5 4.661 A A 3 2 3.036 2.873 0.777 1.720 AA_DT4DC5:DG2DA3_AA 4 7.839 -12.719 35.269 2.373 -0.176 7.190 31.554 A A 5 6 -1.909 A A 2 1 7.184 -1.036 -0.884 1.325 AA_DC5DG6:DC1DG2_AA 5 -3.211 5.916 31.378 2.860 0.312 chem_comp_atom chem_comp_bond database_2 pdbx_unobs_or_zero_occ_atoms struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Advisory Data collection Database references Derived calculations Refinement description 1 0 1997-04-29 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y NDB 1997-03-25 REL BDA 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] HOH water 152D DDF045 PDB experimental model BDA 7 2 BDA BDA 7 A HOH 8 3 HOH HOH 8 A HOH 9 3 HOH HOH 9 A HOH 10 3 HOH HOH 10 A HOH 11 3 HOH HOH 11 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A 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 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8_665 -y+1,-x+1,-z+1/2 crystal symmetry operation 28.2700000000 28.2700000000 26.8850000000 1 3.83 0.60 118.90 122.73 A A A N1 C2 O2 DC DC DC 1 1 1 N 1 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -4.47 0.60 122.30 117.83 A A A N3 C2 O2 DT DT DT 4 4 4 N 1 -4.27 0.60 122.90 118.63 A A A C6 C5 C7 DT DT DT 4 4 4 N 1 4.34 0.60 118.90 123.24 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 -4.26 0.70 121.90 117.64 A A A N3 C2 O2 DC DC DC 5 5 5 N PARDNA.PRO TOPDNA.PRO 0.3140000 0.1990000 0.1990000 2.200 10.000 1061 10.000 97.400 RANDOM 1 3.000 MOLECULAR REPLACEMENT DDF045 TR isotropic TR isotropic 2.200 10.000 8 170 42 120 0 0.014 3.10 0.2850000 2.30 111 82.80 fix fix 1.800 12.000 1AGL 11192 2058 0.000 0.0700000 1 5.5000 6.760 93.000 refinement X-PLOR data collection ADSC STRUCTURE OF A DNA-BISDAUNOMYCIN COMPLEX 1 N N 2 N N 3 N N covale 1.355 none A BDA 7 B C9A BDA 1_555 A BDA 7 B C9A BDA 8_665 covale 1.360 none A BDA 7 B C9B BDA 1_555 A BDA 7 B C9B BDA 8_665 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 6 A N1 DG 6 8_665 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 6 A O6 DG 6 8_665 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 6 A N2 DG 6 8_665 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 8_665 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 8_665 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 5 A N4 DC 5 8_665 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 4 A N3 DT 4 8_665 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 4 A O4 DT 4 8_665 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 3 A N1 DA 3 8_665 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 3 A N6 DA 3 8_665 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 2 A N1 DG 2 8_665 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 8_665 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 2 8_665 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 1 A N3 DC 1 8_665 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 1 A O2 DC 1 8_665 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 1 A N4 DC 1 8_665 DNA RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA 1AGL PDB 1 1AGL 1 6 1AGL 1 6 1AGL A 1 1 6 BINDING SITE FOR RESIDUE BDA A 7 A BDA 7 Software 8 A DC 1 A DC 1 8 8_665 A DG 2 A DG 2 8 8_665 A DA 3 A DA 3 8 8_665 A DT 4 A DT 4 8 8_665 A DT 4 A DT 4 8 1_555 A DC 5 A DC 5 8 1_555 A DG 6 A DG 6 8 1_555 A HOH 11 C HOH 8 1_555 92 P 41 21 2