data_4YVH # _model_server_result.job_id OH-xednIwiKU9nu_OG2O0w _model_server_result.datetime_utc '2024-10-19 07:30:22' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4yvh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4YVH # _exptl.entry_id 4YVH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4YVH _cell.length_a 93.766 _cell.length_b 93.766 _cell.length_c 177.907 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YVH _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 46.883 27.067913 59.302333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H23 N7 O5' _chem_comp.formula_weight 381.387 _chem_comp.id SFG _chem_comp.mon_nstd_flag . _chem_comp.name SINEFUNGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADENOSYL-ORNITHINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N CA SFG sing 290 n n N HN1 SFG sing 291 n n N HN2 SFG sing 292 n n CA C SFG sing 293 n n CA CB SFG sing 294 n n CA HA SFG sing 295 n n C O SFG doub 296 n n C OXT SFG sing 297 n n OXT HXT SFG sing 298 n n CB CG SFG sing 299 n n CB HB1 SFG sing 300 n n CB HB2 SFG sing 301 n n CG CD SFG sing 302 n n CG HG1 SFG sing 303 n n CG HG2 SFG sing 304 n n CD NE SFG sing 305 n n CD C5' SFG sing 306 n n CD HD SFG sing 307 n n NE HNE1 SFG sing 308 n n NE HNE2 SFG sing 309 n n C5' C4' SFG sing 310 n n C5' "H5'1" SFG sing 311 n n C5' "H5'2" SFG sing 312 n n C4' O4' SFG sing 313 n n C4' C3' SFG sing 314 n n C4' H4' SFG sing 315 n n O4' C1' SFG sing 316 n n C3' O3' SFG sing 317 n n C3' C2' SFG sing 318 n n C3' H3' SFG sing 319 n n O3' HO3' SFG sing 320 n n C2' O2' SFG sing 321 n n C2' C1' SFG sing 322 n n C2' H2' SFG sing 323 n n O2' HO2' SFG sing 324 n n C1' N9 SFG sing 325 n n C1' H1' SFG sing 326 n n N9 C8 SFG sing 327 n y N9 C4 SFG sing 328 n y C8 N7 SFG doub 329 n y C8 H8 SFG sing 330 n n N7 C5 SFG sing 331 n y C5 C6 SFG sing 332 n y C5 C4 SFG doub 333 n y C6 N6 SFG sing 334 n n C6 N1 SFG doub 335 n y N6 HN61 SFG sing 336 n n N6 HN62 SFG sing 337 n n N1 C2 SFG sing 338 n y C2 N3 SFG doub 339 n y C2 H2 SFG sing 340 n n N3 C4 SFG sing 341 n y # _atom_sites.entry_id 4YVH _atom_sites.fract_transf_matrix[1][1] 0.010665 _atom_sites.fract_transf_matrix[1][2] 0.006157 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012315 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005621 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SFG A 1 301 301 SFG SFG . C 3 HOH A 1 401 356 HOH HOH . C 3 HOH A 2 402 357 HOH HOH . C 3 HOH A 3 403 151 HOH HOH . C 3 HOH A 4 404 213 HOH HOH . C 3 HOH A 5 405 342 HOH HOH . C 3 HOH A 6 406 108 HOH HOH . C 3 HOH A 7 407 86 HOH HOH . C 3 HOH A 8 408 310 HOH HOH . C 3 HOH A 9 409 84 HOH HOH . C 3 HOH A 10 410 291 HOH HOH . C 3 HOH A 11 411 337 HOH HOH . C 3 HOH A 12 412 223 HOH HOH . C 3 HOH A 13 413 123 HOH HOH . C 3 HOH A 14 414 209 HOH HOH . C 3 HOH A 15 415 153 HOH HOH . C 3 HOH A 16 416 102 HOH HOH . C 3 HOH A 17 417 312 HOH HOH . C 3 HOH A 18 418 142 HOH HOH . C 3 HOH A 19 419 331 HOH HOH . C 3 HOH A 20 420 101 HOH HOH . C 3 HOH A 21 421 348 HOH HOH . C 3 HOH A 22 422 372 HOH HOH . C 3 HOH A 23 423 79 HOH HOH . C 3 HOH A 24 424 49 HOH HOH . C 3 HOH A 25 425 128 HOH HOH . C 3 HOH A 26 426 35 HOH HOH . C 3 HOH A 27 427 129 HOH HOH . C 3 HOH A 28 428 136 HOH HOH . C 3 HOH A 29 429 57 HOH HOH . C 3 HOH A 30 430 187 HOH HOH . C 3 HOH A 31 431 130 HOH HOH . C 3 HOH A 32 432 141 HOH HOH . C 3 HOH A 33 433 115 HOH HOH . C 3 HOH A 34 434 328 HOH HOH . C 3 HOH A 35 435 100 HOH HOH . C 3 HOH A 36 436 124 HOH HOH . C 3 HOH A 37 437 257 HOH HOH . C 3 HOH A 38 438 183 HOH HOH . C 3 HOH A 39 439 14 HOH HOH . C 3 HOH A 40 440 80 HOH HOH . C 3 HOH A 41 441 200 HOH HOH . C 3 HOH A 42 442 287 HOH HOH . C 3 HOH A 43 443 323 HOH HOH . C 3 HOH A 44 444 133 HOH HOH . C 3 HOH A 45 445 16 HOH HOH . C 3 HOH A 46 446 32 HOH HOH . C 3 HOH A 47 447 6 HOH HOH . C 3 HOH A 48 448 146 HOH HOH . C 3 HOH A 49 449 109 HOH HOH . C 3 HOH A 50 450 13 HOH HOH . C 3 HOH A 51 451 158 HOH HOH . C 3 HOH A 52 452 288 HOH HOH . C 3 HOH A 53 453 87 HOH HOH . C 3 HOH A 54 454 247 HOH HOH . C 3 HOH A 55 455 8 HOH HOH . C 3 HOH A 56 456 179 HOH HOH . C 3 HOH A 57 457 27 HOH HOH . C 3 HOH A 58 458 382 HOH HOH . C 3 HOH A 59 459 218 HOH HOH . C 3 HOH A 60 460 118 HOH HOH . C 3 HOH A 61 461 47 HOH HOH . C 3 HOH A 62 462 54 HOH HOH . C 3 HOH A 63 463 207 HOH HOH . C 3 HOH A 64 464 374 HOH HOH . C 3 HOH A 65 465 40 HOH HOH . C 3 HOH A 66 466 1 HOH HOH . C 3 HOH A 67 467 62 HOH HOH . C 3 HOH A 68 468 293 HOH HOH . C 3 HOH A 69 469 7 HOH HOH . C 3 HOH A 70 470 91 HOH HOH . C 3 HOH A 71 471 59 HOH HOH . C 3 HOH A 72 472 55 HOH HOH . C 3 HOH A 73 473 53 HOH HOH . C 3 HOH A 74 474 17 HOH HOH . C 3 HOH A 75 475 292 HOH HOH . C 3 HOH A 76 476 149 HOH HOH . C 3 HOH A 77 477 58 HOH HOH . C 3 HOH A 78 478 39 HOH HOH . C 3 HOH A 79 479 159 HOH HOH . C 3 HOH A 80 480 3 HOH HOH . C 3 HOH A 81 481 334 HOH HOH . C 3 HOH A 82 482 44 HOH HOH . C 3 HOH A 83 483 31 HOH HOH . C 3 HOH A 84 484 308 HOH HOH . C 3 HOH A 85 485 74 HOH HOH . C 3 HOH A 86 486 23 HOH HOH . C 3 HOH A 87 487 85 HOH HOH . C 3 HOH A 88 488 63 HOH HOH . C 3 HOH A 89 489 45 HOH HOH . C 3 HOH A 90 490 29 HOH HOH . C 3 HOH A 91 491 265 HOH HOH . C 3 HOH A 92 492 11 HOH HOH . C 3 HOH A 93 493 96 HOH HOH . C 3 HOH A 94 494 165 HOH HOH . C 3 HOH A 95 495 25 HOH HOH . C 3 HOH A 96 496 378 HOH HOH . C 3 HOH A 97 497 20 HOH HOH . C 3 HOH A 98 498 30 HOH HOH . C 3 HOH A 99 499 132 HOH HOH . C 3 HOH A 100 500 95 HOH HOH . C 3 HOH A 101 501 116 HOH HOH . C 3 HOH A 102 502 48 HOH HOH . C 3 HOH A 103 503 36 HOH HOH . C 3 HOH A 104 504 22 HOH HOH . C 3 HOH A 105 505 10 HOH HOH . C 3 HOH A 106 506 180 HOH HOH . C 3 HOH A 107 507 83 HOH HOH . C 3 HOH A 108 508 191 HOH HOH . C 3 HOH A 109 509 332 HOH HOH . C 3 HOH A 110 510 152 HOH HOH . C 3 HOH A 111 511 316 HOH HOH . C 3 HOH A 112 512 184 HOH HOH . C 3 HOH A 113 513 18 HOH HOH . C 3 HOH A 114 514 60 HOH HOH . C 3 HOH A 115 515 88 HOH HOH . C 3 HOH A 116 516 33 HOH HOH . C 3 HOH A 117 517 314 HOH HOH . C 3 HOH A 118 518 76 HOH HOH . C 3 HOH A 119 519 66 HOH HOH . C 3 HOH A 120 520 114 HOH HOH . C 3 HOH A 121 521 78 HOH HOH . C 3 HOH A 122 522 42 HOH HOH . C 3 HOH A 123 523 37 HOH HOH . C 3 HOH A 124 524 134 HOH HOH . C 3 HOH A 125 525 51 HOH HOH . C 3 HOH A 126 526 289 HOH HOH . C 3 HOH A 127 527 164 HOH HOH . C 3 HOH A 128 528 90 HOH HOH . C 3 HOH A 129 529 131 HOH HOH . C 3 HOH A 130 530 380 HOH HOH . C 3 HOH A 131 531 112 HOH HOH . C 3 HOH A 132 532 304 HOH HOH . C 3 HOH A 133 533 61 HOH HOH . C 3 HOH A 134 534 97 HOH HOH . C 3 HOH A 135 535 281 HOH HOH . C 3 HOH A 136 536 311 HOH HOH . C 3 HOH A 137 537 9 HOH HOH . C 3 HOH A 138 538 283 HOH HOH . C 3 HOH A 139 539 188 HOH HOH . C 3 HOH A 140 540 64 HOH HOH . C 3 HOH A 141 541 73 HOH HOH . C 3 HOH A 142 542 172 HOH HOH . C 3 HOH A 143 543 105 HOH HOH . C 3 HOH A 144 544 28 HOH HOH . C 3 HOH A 145 545 43 HOH HOH . C 3 HOH A 146 546 68 HOH HOH . C 3 HOH A 147 547 175 HOH HOH . C 3 HOH A 148 548 5 HOH HOH . C 3 HOH A 149 549 26 HOH HOH . C 3 HOH A 150 550 135 HOH HOH . C 3 HOH A 151 551 50 HOH HOH . C 3 HOH A 152 552 34 HOH HOH . C 3 HOH A 153 553 41 HOH HOH . C 3 HOH A 154 554 266 HOH HOH . C 3 HOH A 155 555 38 HOH HOH . C 3 HOH A 156 556 139 HOH HOH . C 3 HOH A 157 557 117 HOH HOH . C 3 HOH A 158 558 296 HOH HOH . C 3 HOH A 159 559 70 HOH HOH . C 3 HOH A 160 560 121 HOH HOH . C 3 HOH A 161 561 98 HOH HOH . C 3 HOH A 162 562 110 HOH HOH . C 3 HOH A 163 563 286 HOH HOH . C 3 HOH A 164 564 185 HOH HOH . C 3 HOH A 165 565 381 HOH HOH . C 3 HOH A 166 566 375 HOH HOH . C 3 HOH A 167 567 12 HOH HOH . C 3 HOH A 168 568 56 HOH HOH . C 3 HOH A 169 569 285 HOH HOH . C 3 HOH A 170 570 363 HOH HOH . C 3 HOH A 171 571 77 HOH HOH . C 3 HOH A 172 572 15 HOH HOH . C 3 HOH A 173 573 282 HOH HOH . C 3 HOH A 174 574 313 HOH HOH . C 3 HOH A 175 575 358 HOH HOH . C 3 HOH A 176 576 327 HOH HOH . C 3 HOH A 177 577 280 HOH HOH . C 3 HOH A 178 578 138 HOH HOH . C 3 HOH A 179 579 351 HOH HOH . C 3 HOH A 180 580 81 HOH HOH . C 3 HOH A 181 581 373 HOH HOH . C 3 HOH A 182 582 345 HOH HOH . C 3 HOH A 183 583 71 HOH HOH . C 3 HOH A 184 584 111 HOH HOH . C 3 HOH A 185 585 137 HOH HOH . C 3 HOH A 186 586 377 HOH HOH . C 3 HOH A 187 587 321 HOH HOH . C 3 HOH A 188 588 284 HOH HOH . C 3 HOH A 189 589 343 HOH HOH . C 3 HOH A 190 590 113 HOH HOH . C 3 HOH A 191 591 210 HOH HOH . C 3 HOH A 192 592 196 HOH HOH . C 3 HOH A 193 593 305 HOH HOH . C 3 HOH A 194 594 383 HOH HOH . C 3 HOH A 195 595 190 HOH HOH . C 3 HOH A 196 596 340 HOH HOH . C 3 HOH A 197 597 359 HOH HOH . C 3 HOH A 198 598 333 HOH HOH . C 3 HOH A 199 599 106 HOH HOH . C 3 HOH A 200 600 143 HOH HOH . C 3 HOH A 201 601 259 HOH HOH . C 3 HOH A 202 602 261 HOH HOH . C 3 HOH A 203 603 157 HOH HOH . C 3 HOH A 204 604 364 HOH HOH . C 3 HOH A 205 605 239 HOH HOH . C 3 HOH A 206 606 120 HOH HOH . C 3 HOH A 207 607 335 HOH HOH . C 3 HOH A 208 608 167 HOH HOH . C 3 HOH A 209 609 361 HOH HOH . C 3 HOH A 210 610 344 HOH HOH . C 3 HOH A 211 611 347 HOH HOH . C 3 HOH A 212 612 82 HOH HOH . C 3 HOH A 213 613 329 HOH HOH . C 3 HOH A 214 614 19 HOH HOH . C 3 HOH A 215 615 346 HOH HOH . C 3 HOH A 216 616 92 HOH HOH . C 3 HOH A 217 617 238 HOH HOH . C 3 HOH A 218 618 24 HOH HOH . C 3 HOH A 219 619 354 HOH HOH . C 3 HOH A 220 620 366 HOH HOH . C 3 HOH A 221 621 379 HOH HOH . C 3 HOH A 222 622 370 HOH HOH . C 3 HOH A 223 623 353 HOH HOH . C 3 HOH A 224 624 324 HOH HOH . C 3 HOH A 225 625 181 HOH HOH . C 3 HOH A 226 626 338 HOH HOH . C 3 HOH A 227 627 65 HOH HOH . C 3 HOH A 228 628 72 HOH HOH . C 3 HOH A 229 629 315 HOH HOH . C 3 HOH A 230 630 318 HOH HOH . C 3 HOH A 231 631 376 HOH HOH . C 3 HOH A 232 632 270 HOH HOH . C 3 HOH A 233 633 21 HOH HOH . C 3 HOH A 234 634 369 HOH HOH . C 3 HOH A 235 635 262 HOH HOH . C 3 HOH A 236 636 365 HOH HOH . C 3 HOH A 237 637 349 HOH HOH . C 3 HOH A 238 638 368 HOH HOH . C 3 HOH A 239 639 336 HOH HOH . C 3 HOH A 240 640 264 HOH HOH . C 3 HOH A 241 641 371 HOH HOH . C 3 HOH A 242 642 339 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N SFG . . . B 2 30.688 18.081 15.723 1 23.77 ? N SFG 301 A 1 HETATM 2 C CA SFG . . . B 2 29.489 17.482 16.325 1 23.8 ? CA SFG 301 A 1 HETATM 3 C C SFG . . . B 2 28.657 18.624 16.915 1 29.91 ? C SFG 301 A 1 HETATM 4 O O SFG . . . B 2 27.418 18.563 16.756 1 30.48 ? O SFG 301 A 1 HETATM 5 O OXT SFG . . . B 2 29.276 19.541 17.497 1 38.79 ? OXT SFG 301 A 1 HETATM 6 C CB SFG . . . B 2 29.916 16.526 17.443 1 21.04 ? CB SFG 301 A 1 HETATM 7 C CG SFG . . . B 2 30.271 15.117 16.953 1 15.93 ? CG SFG 301 A 1 HETATM 8 C CD SFG . . . B 2 30.716 14.256 18.14 1 14.37 ? CD SFG 301 A 1 HETATM 9 N NE SFG . . . B 2 32.096 14.603 18.525 1 15.89 ? NE SFG 301 A 1 HETATM 10 C C5' SFG . . . B 2 30.649 12.762 17.807 1 15.4 ? C5' SFG 301 A 1 HETATM 11 C C4' SFG . . . B 2 29.293 12.146 18.17 1 15.66 ? C4' SFG 301 A 1 HETATM 12 O O4' SFG . . . B 2 29.061 12.228 19.582 1 15.75 ? O4' SFG 301 A 1 HETATM 13 C C3' SFG . . . B 2 28.091 12.865 17.558 1 16.67 ? C3' SFG 301 A 1 HETATM 14 O O3' SFG . . . B 2 27.947 12.41 16.21 1 18.94 ? O3' SFG 301 A 1 HETATM 15 C C2' SFG . . . B 2 26.967 12.317 18.441 1 16.42 ? C2' SFG 301 A 1 HETATM 16 O O2' SFG . . . B 2 26.512 11.035 17.995 1 18.24 ? O2' SFG 301 A 1 HETATM 17 C C1' SFG . . . B 2 27.643 12.168 19.808 1 14.64 ? C1' SFG 301 A 1 HETATM 18 N N9 SFG . . . B 2 27.314 13.276 20.735 1 15.94 ? N9 SFG 301 A 1 HETATM 19 C C8 SFG . . . B 2 28.149 14.207 21.195 1 18.27 ? C8 SFG 301 A 1 HETATM 20 N N7 SFG . . . B 2 27.508 14.992 22.059 1 14.68 ? N7 SFG 301 A 1 HETATM 21 C C5 SFG . . . B 2 26.252 14.561 22.147 1 14.46 ? C5 SFG 301 A 1 HETATM 22 C C6 SFG . . . B 2 25.145 14.957 22.886 1 15.27 ? C6 SFG 301 A 1 HETATM 23 N N6 SFG . . . B 2 25.219 15.997 23.717 1 15.9 ? N6 SFG 301 A 1 HETATM 24 N N1 SFG . . . B 2 24.006 14.264 22.74 1 14.58 ? N1 SFG 301 A 1 HETATM 25 C C2 SFG . . . B 2 23.925 13.231 21.917 1 14.24 ? C2 SFG 301 A 1 HETATM 26 N N3 SFG . . . B 2 24.957 12.824 21.196 1 14.66 ? N3 SFG 301 A 1 HETATM 27 C C4 SFG . . . B 2 26.126 13.47 21.297 1 14.76 ? C4 SFG 301 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #