0.012718 0.000000 0.007904 0.000000 0.022276 0.000000 0.000000 0.000000 0.028238 0.00000 0.00000 0.00000 0009-0005-2321-7514 Tsai, C.J. 0009-0009-2286-839X Huang, Y.Z. 0000-0003-4170-1527 Hou, M.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 121.86 90.00 78.631 44.892 41.695 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 C5 H11 N O2 117.146 D-VALINE D-peptide linking C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 n N-METHYLVALINE L-peptide linking C4 H10 O3 106.120 DI(HYDROXYETHYL)ETHER non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C16 H12 N2 O6 328.276 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE PHENOXAZINE non-polymer C3 H7 N O2 89.093 n SARCOSINE peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 N N 145 R C N 146 N C N 147 N C N 148 N C N 149 N C N 150 N O N 151 N O N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N C N 164 N O N 165 N C N 166 N O N 167 N C N 168 N O N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N O N 178 N H N 179 N H N 180 N N N 181 N C N 182 S C N 183 N C N 184 N C N 185 N C N 186 N C N 187 N O N 188 N O N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N C N 203 N O N 204 N C N 205 N O N 206 N C N 207 N C N 208 N O 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 N N 220 S C N 221 N C N 222 N O N 223 N C N 224 N C N 225 N C N 226 N O N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N C N 237 N C N 238 N O N 239 N C N 240 N N N 241 N C N 242 N O N 243 N C N 244 N O Y 245 N C Y 246 N C Y 247 N C Y 248 N C N 249 N C N 250 N O N 251 N N N 252 N C N 253 N C Y 254 N C Y 255 N C N 256 N C N 257 N C N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N O N 269 N O N 270 N H N 271 N H N 272 N N N 273 N C N 274 N C N 275 N O N 276 N C N 277 N O N 278 N H 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 N N 286 S C N 287 N C N 288 N O N 289 R C N 290 N O N 291 N C N 292 N O N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 1 N sing N 2 N sing N 3 N doub 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 sing 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing 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 doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing 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 sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing 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 doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub 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 N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub 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 N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 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 sing 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 sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N doub N 239 N sing N 240 N doub N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N doub N 248 N sing N 249 N sing N 250 N sing Y 251 N doub Y 252 N sing N 253 N sing Y 254 N sing N 255 N sing Y 256 N doub N 257 N sing N 258 N sing Y 259 N sing N 260 N doub N 261 N doub N 262 N sing N 263 N sing Y 264 N doub N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N doub 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 doub N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing To Be Published 0353 Crystal structure of Actinomycin D with d(AGGGCGCGT/AGGGCGCGT) 0009-0009-2286-839X 0009-0009-2286-839X 0000-0003-4170-1527 10.2210/pdb9wpj/pdb pdb_00009wpj 298 1 N PIXEL 2022-10-05 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 1.0 1.0 TPS 07A NSRRC 1.0 SYNCHROTRON NSRRC BEAMLINE TPS 07A 1291.446 Actinomycin D 4 syn polymer 2467.629 DNA (5'-D(*AP*GP*GP*CP*GP*CP*GP*T)-3') 2 syn polymer 106.120 DI(HYDROXYETHYL)ETHER 1 syn non-polymer 92.094 GLYCEROL 1 syn non-polymer 18.015 water 218 nat water no yes T(DVA)P(SAR)(MVA)(PXZ)T(DVA)P(SAR)(MVA) TVPGVXTVPGV C,D,E,F polypeptide(L) no no (DA)(DG)(DG)(DC)(DG)(DC)(DG)(DT) AGGCGCGT A,B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n 1 3.07 59.96 VAPOR DIFFUSION, SITTING DROP 7.0 Glycerol, PEG500 MME, Bis-Tris buffer, Ammonium sulfate 298 15.160 1 19 A 3 B 6 2.245 A_DG3:DC6_B 1 16.925 -0.358 0.477 -0.087 -5.455 1 19 A 4 B 5 3.624 A_DC4:DG5_B 2 17.335 0.317 0.678 -0.184 7.838 1 19 A 5 B 4 3.512 A_DG5:DC4_B 3 15.616 -0.349 0.703 -0.180 -14.900 1 19 A 6 B 3 2.919 A_DC6:DG3_B 4 18.213 0.540 0.440 -0.054 2.769 28.714 A A 4 5 76.567 B B 5 4 3.366 27.912 -0.135 2.022 AA_DC4DG5:DC4DG5_BB 1 -0.119 0.327 6.805 -5.615 0.232 repository Initial release 1 0 2026-09-09 Taiwan Ministry of Science and Technology (MoST, Taiwan) 113-2311-B-005-006-MY3 Taiwan Ministry of Science and Technology (MoST, Taiwan) 113-2311-M-005-016-MY3 mhho@dragon.nchu.edu.tw 0000-0003-4170-1527 Ming Hon Hou principal investigator/group leader N PDBJ Y PDBJ 2025-09-09 REL REL 1 D O HOH 218 6.02 1 D O HOH 219 7.13 1 D O HOH 220 8.25 1 A O HOH 267 5.81 1 A O HOH 268 6.04 1 A O HOH 269 6.64 1 A O HOH 270 6.81 1 A O HOH 271 6.98 1 A O HOH 272 7.28 1 A O HOH 273 7.92 1 A O HOH 274 10.63 1 E O HOH 114 5.98 1 E O HOH 115 6.38 1 E O HOH 116 7.17 1 F O HOH 114 6.28 1 F O HOH 115 8.46 1 F O HOH 116 8.69 1 F O HOH 117 9.59 1 B O HOH 158 5.81 1 B O HOH 159 5.87 1 B O HOH 160 6.08 1 B O HOH 161 6.23 1 B O HOH 162 6.48 1 B O HOH 163 6.52 1 B O HOH 164 6.62 1 B O HOH 165 6.97 1 B O HOH 166 7.09 1 B O HOH 167 7.16 1 B O HOH 168 7.53 1 B O HOH 169 7.61 1 B O HOH 170 7.78 1 B O HOH 171 8.85 1 B O HOH 172 8.92 1 B O HOH 173 9.26 1 B O HOH 174 10.30 1 B O HOH 175 11.21 1 B O HOH 176 11.82 1 B O HOH 177 12.03 1 B O HOH 178 12.25 1 B O HOH 179 13.42 PXZ PXZ SUBJECT OF INVESTIGATION PEG DI(HYDROXYETHYL)ETHER GOL GLYCEROL HOH water 1890 Streptomyces antibioticus sample 1 11 9606 Homo sapiens sample 1 8 ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES) Y Y Ideal B form DNA Other experimental model C SAR 4 Named protein modification A SAR 4 GLY SAR 1 1_555 Methylation C MVA 5 Named protein modification A MVA 5 VAL MVA 1 1_555 Methylation C SAR 10 Named protein modification A SAR 10 GLY SAR 1 1_555 Methylation C MVA 11 Named protein modification A MVA 11 VAL MVA 1 1_555 Methylation D SAR 4 Named protein modification B SAR 4 GLY SAR 1 1_555 Methylation D MVA 5 Named protein modification B MVA 5 VAL MVA 1 1_555 Methylation D SAR 10 Named protein modification B SAR 10 GLY SAR 1 1_555 Methylation D MVA 11 Named protein modification B MVA 11 VAL MVA 1 1_555 Methylation E SAR 4 Named protein modification D SAR 4 GLY SAR 1 1_555 Methylation E MVA 5 Named protein modification D MVA 5 VAL MVA 1 1_555 Methylation E SAR 10 Named protein modification D SAR 10 GLY SAR 1 1_555 Methylation E MVA 11 Named protein modification D MVA 11 VAL MVA 1 1_555 Methylation F SAR 4 Named protein modification E SAR 4 GLY SAR 1 1_555 Methylation F MVA 5 Named protein modification E MVA 5 VAL MVA 1 1_555 Methylation F SAR 10 Named protein modification E SAR 10 GLY SAR 1 1_555 Methylation F MVA 11 Named protein modification E MVA 11 VAL MVA 1 1_555 Methylation C PXZ 6 Non-standard residue A PXZ 6 PXZ 1 1_555 None D PXZ 6 Non-standard residue B PXZ 6 PXZ 1 1_555 None E PXZ 6 Non-standard residue D PXZ 6 PXZ 1 1_555 None F PXZ 6 Non-standard residue E PXZ 6 PXZ 1 1_555 None C THR 1 Non-standard linkage OG1 A THR 1 C MVA 5 C A MVA 5 1_555 1_555 None C THR 1 Non-standard linkage N A THR 1 C PXZ 6 C0 A PXZ 6 1_555 1_555 None C THR 7 Non-standard linkage OG1 A THR 7 C MVA 11 C A MVA 11 1_555 1_555 None D THR 1 Non-standard linkage OG1 B THR 1 D MVA 5 C B MVA 5 1_555 1_555 None D THR 1 Non-standard linkage N B THR 1 D PXZ 6 C0 B PXZ 6 1_555 1_555 None D THR 7 Non-standard linkage OG1 B THR 7 D MVA 11 C B MVA 11 1_555 1_555 None E THR 1 Non-standard linkage OG1 D THR 1 E MVA 5 C D MVA 5 1_555 1_555 None E THR 1 Non-standard linkage N D THR 1 E PXZ 6 C0 D PXZ 6 1_555 1_555 None E THR 7 Non-standard linkage OG1 D THR 7 E MVA 11 C D MVA 11 1_555 1_555 None F THR 1 Non-standard linkage OG1 E THR 1 F MVA 5 C E MVA 5 1_555 1_555 None F THR 1 Non-standard linkage N E THR 1 F PXZ 6 C0 E PXZ 6 1_555 1_555 None F THR 7 Non-standard linkage OG1 E THR 7 F MVA 11 C E MVA 11 1_555 1_555 None Antibiotic ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ) Actinomycin D Polypeptide PEG 1 3 PEG PEG 101 D GOL 2 4 GOL GOL 101 A HOH 13 5 HOH HOH 101 C HOH 20 5 HOH HOH 102 C HOH 43 5 HOH HOH 103 C HOH 30 5 HOH HOH 104 C HOH 60 5 HOH HOH 105 C HOH 156 5 HOH HOH 106 C HOH 84 5 HOH HOH 107 C HOH 62 5 HOH HOH 108 C HOH 109 5 HOH HOH 109 C HOH 102 5 HOH HOH 110 C HOH 81 5 HOH HOH 111 C HOH 40 5 HOH HOH 112 C HOH 45 5 HOH HOH 201 D HOH 41 5 HOH HOH 202 D HOH 42 5 HOH HOH 203 D HOH 80 5 HOH HOH 204 D HOH 111 5 HOH HOH 205 D HOH 110 5 HOH HOH 206 D HOH 87 5 HOH HOH 207 D HOH 222 5 HOH HOH 208 D HOH 89 5 HOH HOH 209 D HOH 52 5 HOH HOH 210 D HOH 209 5 HOH HOH 211 D HOH 101 5 HOH HOH 212 D HOH 79 5 HOH HOH 213 D HOH 88 5 HOH HOH 214 D HOH 169 5 HOH HOH 215 D HOH 174 5 HOH HOH 216 D HOH 140 5 HOH HOH 217 D HOH 145 5 HOH HOH 218 D HOH 112 5 HOH HOH 219 D HOH 141 5 HOH HOH 220 D HOH 57 5 HOH HOH 201 A HOH 61 5 HOH HOH 202 A HOH 98 5 HOH HOH 203 A HOH 4 5 HOH HOH 204 A HOH 36 5 HOH HOH 205 A HOH 69 5 HOH HOH 206 A HOH 11 5 HOH HOH 207 A HOH 23 5 HOH HOH 208 A HOH 75 5 HOH HOH 209 A HOH 15 5 HOH HOH 210 A HOH 9 5 HOH HOH 211 A HOH 12 5 HOH HOH 212 A HOH 99 5 HOH HOH 213 A HOH 215 5 HOH HOH 214 A HOH 33 5 HOH HOH 215 A HOH 22 5 HOH HOH 216 A HOH 224 5 HOH HOH 217 A HOH 38 5 HOH HOH 218 A HOH 49 5 HOH HOH 219 A HOH 207 5 HOH HOH 220 A HOH 151 5 HOH HOH 221 A HOH 123 5 HOH HOH 222 A HOH 63 5 HOH HOH 223 A HOH 39 5 HOH HOH 224 A HOH 29 5 HOH HOH 225 A HOH 70 5 HOH HOH 226 A HOH 46 5 HOH HOH 227 A HOH 44 5 HOH HOH 228 A HOH 97 5 HOH HOH 229 A HOH 86 5 HOH HOH 230 A HOH 95 5 HOH HOH 231 A HOH 122 5 HOH HOH 232 A HOH 166 5 HOH HOH 233 A HOH 205 5 HOH HOH 234 A HOH 208 5 HOH HOH 235 A HOH 171 5 HOH HOH 236 A HOH 58 5 HOH HOH 237 A HOH 66 5 HOH HOH 238 A HOH 26 5 HOH HOH 239 A HOH 94 5 HOH HOH 240 A HOH 117 5 HOH HOH 241 A HOH 187 5 HOH HOH 242 A HOH 202 5 HOH HOH 243 A HOH 185 5 HOH HOH 244 A HOH 168 5 HOH HOH 245 A HOH 186 5 HOH HOH 246 A HOH 190 5 HOH HOH 247 A HOH 35 5 HOH HOH 248 A HOH 78 5 HOH HOH 249 A HOH 201 5 HOH HOH 250 A HOH 118 5 HOH HOH 251 A HOH 223 5 HOH HOH 252 A HOH 96 5 HOH HOH 253 A HOH 221 5 HOH HOH 254 A HOH 100 5 HOH HOH 255 A HOH 194 5 HOH HOH 256 A HOH 124 5 HOH HOH 257 A HOH 146 5 HOH HOH 258 A HOH 82 5 HOH HOH 259 A HOH 180 5 HOH HOH 260 A HOH 93 5 HOH HOH 261 A HOH 155 5 HOH HOH 262 A HOH 219 5 HOH HOH 263 A HOH 198 5 HOH HOH 264 A HOH 204 5 HOH HOH 265 A HOH 147 5 HOH HOH 266 A HOH 137 5 HOH HOH 267 A HOH 149 5 HOH HOH 268 A HOH 148 5 HOH HOH 269 A HOH 138 5 HOH HOH 270 A HOH 220 5 HOH HOH 271 A HOH 152 5 HOH HOH 272 A HOH 139 5 HOH HOH 273 A HOH 193 5 HOH HOH 274 A HOH 59 5 HOH HOH 101 E HOH 50 5 HOH HOH 102 E HOH 77 5 HOH HOH 103 E HOH 32 5 HOH HOH 104 E HOH 27 5 HOH HOH 105 E HOH 10 5 HOH HOH 106 E HOH 161 5 HOH HOH 107 E HOH 127 5 HOH HOH 108 E HOH 48 5 HOH HOH 109 E HOH 150 5 HOH HOH 110 E HOH 55 5 HOH HOH 111 E HOH 7 5 HOH HOH 112 E HOH 225 5 HOH HOH 113 E HOH 135 5 HOH HOH 114 E HOH 103 5 HOH HOH 115 E HOH 203 5 HOH HOH 116 E HOH 67 5 HOH HOH 101 F HOH 68 5 HOH HOH 102 F HOH 64 5 HOH HOH 103 F HOH 3 5 HOH HOH 104 F HOH 19 5 HOH HOH 105 F HOH 119 5 HOH HOH 106 F HOH 125 5 HOH HOH 107 F HOH 129 5 HOH HOH 108 F HOH 130 5 HOH HOH 109 F HOH 16 5 HOH HOH 110 F HOH 54 5 HOH HOH 111 F HOH 53 5 HOH HOH 112 F HOH 51 5 HOH HOH 113 F HOH 206 5 HOH HOH 114 F HOH 173 5 HOH HOH 115 F HOH 226 5 HOH HOH 116 F HOH 170 5 HOH HOH 117 F HOH 8 5 HOH HOH 101 B HOH 14 5 HOH HOH 102 B HOH 25 5 HOH HOH 103 B HOH 56 5 HOH HOH 104 B HOH 71 5 HOH HOH 105 B HOH 6 5 HOH HOH 106 B HOH 1 5 HOH HOH 107 B HOH 177 5 HOH HOH 108 B HOH 120 5 HOH HOH 109 B HOH 128 5 HOH HOH 110 B HOH 230 5 HOH HOH 111 B HOH 160 5 HOH HOH 112 B HOH 34 5 HOH HOH 113 B HOH 2 5 HOH HOH 114 B HOH 126 5 HOH HOH 115 B HOH 18 5 HOH HOH 116 B HOH 211 5 HOH HOH 117 B HOH 21 5 HOH HOH 118 B HOH 212 5 HOH HOH 119 B HOH 162 5 HOH HOH 120 B HOH 213 5 HOH HOH 121 B HOH 47 5 HOH HOH 122 B HOH 90 5 HOH HOH 123 B HOH 37 5 HOH HOH 124 B HOH 5 5 HOH HOH 125 B HOH 85 5 HOH HOH 126 B HOH 31 5 HOH HOH 127 B HOH 172 5 HOH HOH 128 B HOH 17 5 HOH HOH 129 B HOH 76 5 HOH HOH 130 B HOH 210 5 HOH HOH 131 B HOH 191 5 HOH HOH 132 B HOH 192 5 HOH HOH 133 B HOH 217 5 HOH HOH 134 B HOH 65 5 HOH HOH 135 B HOH 121 5 HOH HOH 136 B HOH 136 5 HOH HOH 137 B HOH 176 5 HOH HOH 138 B HOH 104 5 HOH HOH 139 B HOH 108 5 HOH HOH 140 B HOH 134 5 HOH HOH 141 B HOH 200 5 HOH HOH 142 B HOH 216 5 HOH HOH 143 B HOH 214 5 HOH HOH 144 B HOH 199 5 HOH HOH 145 B HOH 72 5 HOH HOH 146 B HOH 92 5 HOH HOH 147 B HOH 165 5 HOH HOH 148 B HOH 175 5 HOH HOH 149 B HOH 91 5 HOH HOH 150 B HOH 114 5 HOH HOH 151 B HOH 24 5 HOH HOH 152 B HOH 105 5 HOH HOH 153 B HOH 83 5 HOH HOH 154 B HOH 28 5 HOH HOH 155 B HOH 132 5 HOH HOH 156 B HOH 159 5 HOH HOH 157 B HOH 218 5 HOH HOH 158 B HOH 131 5 HOH HOH 159 B HOH 195 5 HOH HOH 160 B HOH 107 5 HOH HOH 161 B HOH 229 5 HOH HOH 162 B HOH 106 5 HOH HOH 163 B HOH 163 5 HOH HOH 164 B HOH 197 5 HOH HOH 165 B HOH 167 5 HOH HOH 166 B HOH 189 5 HOH HOH 167 B HOH 154 5 HOH HOH 168 B HOH 74 5 HOH HOH 169 B HOH 144 5 HOH HOH 170 B HOH 133 5 HOH HOH 171 B HOH 179 5 HOH HOH 172 B HOH 113 5 HOH HOH 173 B HOH 143 5 HOH HOH 174 B HOH 142 5 HOH HOH 175 B HOH 153 5 HOH HOH 176 B HOH 116 5 HOH HOH 177 B HOH 115 5 HOH HOH 178 B HOH 196 5 HOH HOH 179 B THR 1 n 1 THR 1 C DVA 2 n 2 DVA 2 C PRO 3 n 3 PRO 3 C SAR 4 n 4 SAR 4 C MVA 5 n 5 MVA 5 C PXZ 6 n 6 PXZ 6 C THR 7 n 7 THR 7 C DVA 8 n 8 DVA 8 C PRO 9 n 9 PRO 9 C SAR 10 n 10 SAR 10 C MVA 11 n 11 MVA 11 C THR 1 n 1 THR 1 D DVA 2 n 2 DVA 2 D PRO 3 n 3 PRO 3 D SAR 4 n 4 SAR 4 D MVA 5 n 5 MVA 5 D PXZ 6 n 6 PXZ 6 D THR 7 n 7 THR 7 D DVA 8 n 8 DVA 8 D PRO 9 n 9 PRO 9 D SAR 10 n 10 SAR 10 D MVA 11 n 11 MVA 11 D DA 1 n 1 DA 1 A DG 2 n 2 DG 2 A DG 3 n 3 DG 3 A DC 4 n 4 DC 4 A DG 5 n 5 DG 5 A DC 6 n 6 DC 6 A DG 7 n 7 DG 7 A DT 8 n 8 DT 8 A THR 1 n 1 THR 1 E DVA 2 n 2 DVA 2 E PRO 3 n 3 PRO 3 E SAR 4 n 4 SAR 4 E MVA 5 n 5 MVA 5 E PXZ 6 n 6 PXZ 6 E THR 7 n 7 THR 7 E DVA 8 n 8 DVA 8 E PRO 9 n 9 PRO 9 E SAR 10 n 10 SAR 10 E MVA 11 n 11 MVA 11 E THR 1 n 1 THR 1 F DVA 2 n 2 DVA 2 F PRO 3 n 3 PRO 3 F SAR 4 n 4 SAR 4 F MVA 5 n 5 MVA 5 F PXZ 6 n 6 PXZ 6 F THR 7 n 7 THR 7 F DVA 8 n 8 DVA 8 F PRO 9 n 9 PRO 9 F SAR 10 n 10 SAR 10 F MVA 11 n 11 MVA 11 F DA 1 n 1 DA 1 B DG 2 n 2 DG 2 B DG 3 n 3 DG 3 B DC 4 n 4 DC 4 B DG 5 n 5 DG 5 B DC 6 n 6 DC 6 B DG 7 n 7 DG 7 B DT 8 n 8 DT 8 B author_defined_assembly 6 hexameric none 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 HOH 173 N HOH 1 A O5' DA 1 C O5' DA 1 1 Y 1 B O5' DA 1 F O5' DA 1 1 Y 1 D D OG1 O THR MVA 7 11 1.93 1 D D OG1 CA THR MVA 1 5 2.19 1 1.90 0.30 108.30 110.20 A A A O4' C1' N9 DA DA DA 1 1 1 N 0.2701 0.2190 0.2242 1.61 22.52 1472 14617 10.07 90.40 0.24 1 FREE R-VALUE 1.36 MOLECULAR REPLACEMENT 31.09 0.90 1.10 ML FLAT BULK SOLVENT MODEL 1.61 22.52 218 917 13 326 360 0.007 761 1.245 1102 26.440 256 0.043 110 0.009 76 0.3739 0.2773 1.66 134 1216 92.00 0.2817 0.2676 1.72 129 1236 95.00 0.2958 0.2523 1.79 140 1258 96.00 0.3252 0.2437 1.87 149 1226 93.00 0.3110 0.2465 1.97 136 1195 91.00 0.3147 0.2420 2.09 124 1239 95.00 0.3054 0.2443 2.25 154 1236 93.00 0.3390 0.2391 2.48 135 1206 91.00 0.2852 0.2502 2.84 134 1158 87.00 0.2528 0.2017 3.57 123 1097 83.00 0.2009 0.1748 22.52 114 1078 78.00 1.61 30.00 9WPJ 14667 0.989 0.997 0.060 0.039 0.072 1.059 1 10.3 48140 3.3 90.9 0.381 1.61 1.67 1527 0.901 0.973 0.234 0.449 1.055 1 3.5 95.7 0.266 1.67 1.73 1519 0.947 0.986 0.163 0.314 1.077 1 3.5 95.4 0.208 1.73 1.81 1561 0.955 0.988 0.128 0.245 1.079 1 3.5 95.6 0.154 1.81 1.91 1472 0.969 0.992 0.100 0.185 1.062 1 3.2 92.6 0.117 1.91 2.03 1465 0.984 0.996 0.075 0.139 1.082 1 3.3 92.7 0.102 2.03 2.18 1555 0.985 0.996 0.065 0.121 1.041 1 3.4 94.8 0.083 2.18 2.40 1462 0.990 0.997 0.052 0.099 1.056 1 3.3 91.8 0.065 2.40 2.75 1428 0.995 0.999 0.041 0.077 1.017 1 3.1 88.8 0.051 2.75 3.47 1373 0.995 0.999 0.035 0.063 1.073 1 3.0 83.7 0.043 3.47 30.00 1305 0.994 0.999 0.028 0.052 1.044 1 2.8 78.4 refinement PHENIX (2.0_5885: ???) data reduction HKL-2000 data extraction PDB_EXTRACT data scaling HKL-2000 phasing PHENIX N Crystal structure of Actinomycin D with d(AGGCGCGT/AGGCGCGT) 1 N N 1 N N 2 N N 1 N N 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N covale 1.325 both C THR 1 A C THR 1 1_555 C DVA 2 A N DVA 2 1_555 covale 1.371 one C THR 1 A OG1 THR 1 1_555 C MVA 5 A C MVA 5 1_555 covale 1.423 both C THR 1 A N THR 1 1_555 C PXZ 6 A C0 PXZ 6 1_555 covale 1.347 both C DVA 2 A C DVA 2 1_555 C PRO 3 A N PRO 3 1_555 covale 1.333 both C PRO 3 A C PRO 3 1_555 C SAR 4 A N SAR 4 1_555 covale 1.333 both C SAR 4 A C SAR 4 1_555 C MVA 5 A N MVA 5 1_555 covale 1.425 both C PXZ 6 A C0' PXZ 6 1_555 C THR 7 A N THR 7 1_555 covale 1.325 both C THR 7 A C THR 7 1_555 C DVA 8 A N DVA 8 1_555 covale 1.372 one C THR 7 A OG1 THR 7 1_555 C MVA 11 A C MVA 11 1_555 covale 1.347 both C DVA 8 A C DVA 8 1_555 C PRO 9 A N PRO 9 1_555 covale 1.327 both C PRO 9 A C PRO 9 1_555 C SAR 10 A N SAR 10 1_555 covale 1.330 both C SAR 10 A C SAR 10 1_555 C MVA 11 A N MVA 11 1_555 covale 1.326 both D THR 1 B C THR 1 1_555 D DVA 2 B N DVA 2 1_555 covale 1.372 one D THR 1 B OG1 THR 1 1_555 D MVA 5 B C MVA 5 1_555 covale 1.426 both D THR 1 B N THR 1 1_555 D PXZ 6 B C0 PXZ 6 1_555 covale 1.344 both D DVA 2 B C DVA 2 1_555 D PRO 3 B N PRO 3 1_555 covale 1.330 both D PRO 3 B C PRO 3 1_555 D SAR 4 B N SAR 4 1_555 covale 1.338 both D SAR 4 B C SAR 4 1_555 D MVA 5 B N MVA 5 1_555 covale 1.425 both D PXZ 6 B C0' PXZ 6 1_555 D THR 7 B N THR 7 1_555 covale 1.327 both D THR 7 B C THR 7 1_555 D DVA 8 B N DVA 8 1_555 covale 1.372 one D THR 7 B OG1 THR 7 1_555 D MVA 11 B C MVA 11 1_555 covale 1.344 both D DVA 8 B C DVA 8 1_555 D PRO 9 B N PRO 9 1_555 covale 1.330 both D PRO 9 B C PRO 9 1_555 D SAR 10 B N SAR 10 1_555 covale 1.332 both D SAR 10 B C SAR 10 1_555 D MVA 11 B N MVA 11 1_555 covale 1.325 both E THR 1 D C THR 1 1_555 E DVA 2 D N DVA 2 1_555 covale 1.370 one E THR 1 D OG1 THR 1 1_555 E MVA 5 D C MVA 5 1_555 covale 1.427 both E THR 1 D N THR 1 1_555 E PXZ 6 D C0 PXZ 6 1_555 covale 1.348 both E DVA 2 D C DVA 2 1_555 E PRO 3 D N PRO 3 1_555 covale 1.330 both E PRO 3 D C PRO 3 1_555 E SAR 4 D N SAR 4 1_555 covale 1.333 both E SAR 4 D C SAR 4 1_555 E MVA 5 D N MVA 5 1_555 covale 1.426 both E PXZ 6 D C0' PXZ 6 1_555 E THR 7 D N THR 7 1_555 covale 1.324 both E THR 7 D C THR 7 1_555 E DVA 8 D N DVA 8 1_555 covale 1.370 one E THR 7 D OG1 THR 7 1_555 E MVA 11 D C MVA 11 1_555 covale 1.346 both E DVA 8 D C DVA 8 1_555 E PRO 9 D N PRO 9 1_555 covale 1.329 both E PRO 9 D C PRO 9 1_555 E SAR 10 D N SAR 10 1_555 covale 1.338 both E SAR 10 D C SAR 10 1_555 E MVA 11 D N MVA 11 1_555 covale 1.327 both F THR 1 E C THR 1 1_555 F DVA 2 E N DVA 2 1_555 covale 1.370 one F THR 1 E OG1 THR 1 1_555 F MVA 5 E C MVA 5 1_555 covale 1.428 both F THR 1 E N THR 1 1_555 F PXZ 6 E C0 PXZ 6 1_555 covale 1.351 both F DVA 2 E C DVA 2 1_555 F PRO 3 E N PRO 3 1_555 covale 1.333 both F PRO 3 E C PRO 3 1_555 F SAR 4 E N SAR 4 1_555 covale 1.335 both F SAR 4 E C SAR 4 1_555 F MVA 5 E N MVA 5 1_555 covale 1.426 both F PXZ 6 E C0' PXZ 6 1_555 F THR 7 E N THR 7 1_555 covale 1.327 both F THR 7 E C THR 7 1_555 F DVA 8 E N DVA 8 1_555 covale 1.373 one F THR 7 E OG1 THR 7 1_555 F MVA 11 E C MVA 11 1_555 covale 1.344 both F DVA 8 E C DVA 8 1_555 F PRO 9 E N PRO 9 1_555 covale 1.329 both F PRO 9 E C PRO 9 1_555 F SAR 10 E N SAR 10 1_555 covale 1.337 both F SAR 10 E C SAR 10 1_555 F MVA 11 E N MVA 11 1_555 hydrog WATSON-CRICK A DG 3 C N1 DG 3 1_555 B DC 6 F N3 DC 6 1_555 hydrog WATSON-CRICK A DG 3 C N2 DG 3 1_555 B DC 6 F O2 DC 6 1_555 hydrog WATSON-CRICK A DG 3 C O6 DG 3 1_555 B DC 6 F N4 DC 6 1_555 hydrog WATSON-CRICK A DC 4 C N3 DC 4 1_555 B DG 5 F N1 DG 5 1_555 hydrog WATSON-CRICK A DC 4 C N4 DC 4 1_555 B DG 5 F O6 DG 5 1_555 hydrog WATSON-CRICK A DC 4 C O2 DC 4 1_555 B DG 5 F N2 DG 5 1_555 hydrog WATSON-CRICK A DG 5 C N1 DG 5 1_555 B DC 4 F N3 DC 4 1_555 hydrog WATSON-CRICK A DG 5 C N2 DG 5 1_555 B DC 4 F O2 DC 4 1_555 hydrog WATSON-CRICK A DG 5 C O6 DG 5 1_555 B DC 4 F N4 DC 4 1_555 hydrog WATSON-CRICK A DC 6 C N3 DC 6 1_555 B DG 3 F N1 DG 3 1_555 hydrog WATSON-CRICK A DC 6 C N4 DC 6 1_555 B DG 3 F O6 DG 3 1_555 hydrog WATSON-CRICK A DC 6 C O2 DC 6 1_555 B DG 3 F N2 DG 3 1_555 DNA/ANTIBIOTIC Bubble structure, Structure genomics, DNA, DNA-ANTIBIOTIC complex C DVA 2 A DVA 2 1 C PRO 3 A PRO 3 9.61 C PRO 3 A PRO 3 1 C SAR 4 A SAR 4 -1.27 C DVA 8 A DVA 8 1 C PRO 9 A PRO 9 7.11 C PRO 9 A PRO 9 1 C SAR 10 A SAR 10 0.97 D DVA 2 B DVA 2 1 D PRO 3 B PRO 3 8.63 D PRO 3 B PRO 3 1 D SAR 4 B SAR 4 -2.53 D DVA 8 B DVA 8 1 D PRO 9 B PRO 9 7.21 D PRO 9 B PRO 9 1 D SAR 10 B SAR 10 2.48 E DVA 2 D DVA 2 1 E PRO 3 D PRO 3 9.04 E PRO 3 D PRO 3 1 E SAR 4 D SAR 4 -1.01 E DVA 8 D DVA 8 1 E PRO 9 D PRO 9 10.53 E PRO 9 D PRO 9 1 E SAR 10 D SAR 10 0.23 F DVA 2 E DVA 2 1 F PRO 3 E PRO 3 7.59 F PRO 3 E PRO 3 1 F SAR 4 E SAR 4 -2.26 F DVA 8 E DVA 8 1 F PRO 9 E PRO 9 11.61 F PRO 9 E PRO 9 1 F SAR 10 E SAR 10 0.04 9WPJ NOR 1 1 NOR00228 9WPJ PDB 2 1 9WPJ 1 11 9WPJ 1 11 9WPJ C 1 1 11 1 11 9WPJ 1 11 9WPJ D 1 1 11 1 8 9WPJ 1 8 9WPJ A 2 1 8 1 11 9WPJ 1 11 9WPJ E 1 1 11 1 11 9WPJ 1 11 9WPJ F 1 1 11 1 8 9WPJ 1 8 9WPJ B 2 1 8 5 C 1 2 1