data_5YOH # _model_server_result.job_id F1H4KX-yKM30dxlV_j_Ucw _model_server_result.datetime_utc '2024-10-19 21:41:04' _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 5yoh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 5YOH # _exptl.entry_id 5YOH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 149.211 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description METHIONINE _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 95.3 _cell.angle_gamma 90 _cell.entry_id 5YOH _cell.length_a 49.332 _cell.length_b 48.69 _cell.length_c 56.151 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YOH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O ASN 143 A ASN 109 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc2 A O VAL 145 A VAL 111 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 A OD1 ASP 165 A ASP 131 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc4 A OD2 ASP 165 A ASP 131 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc5 A OD2 ASP 176 A ASP 142 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 A OD1 ASP 176 A ASP 142 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc7 A NE2 HIS 239 A HIS 205 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 A OE2 GLU 272 A GLU 238 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc9 A O THR 299 A THR 265 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc10 A OG1 THR 299 A THR 265 1_555 D NA NA . A NA 303 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc11 A OE1 GLU 303 A GLU 269 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc12 A OE2 GLU 303 A GLU 269 1_555 C CO CO . A CO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc13 B CO CO . A CO 301 1_555 E OXT MET . A MET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc14 C CO CO . A CO 302 1_555 E OXT MET . A MET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc15 C CO CO . A CO 302 1_555 E N MET . A MET 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc16 D NA NA . A NA 303 1_555 G O HOH . A HOH 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? # _chem_comp.formula 'C5 H11 N O2 S' _chem_comp.formula_weight 149.211 _chem_comp.id MET _chem_comp.mon_nstd_flag y _chem_comp.name METHIONINE _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # 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 MET sing 231 n n N H MET sing 232 n n N H2 MET sing 233 n n CA C MET sing 234 n n CA CB MET sing 235 n n CA HA MET sing 236 n n C O MET doub 237 n n C OXT MET sing 238 n n CB CG MET sing 239 n n CB HB2 MET sing 240 n n CB HB3 MET sing 241 n n CG SD MET sing 242 n n CG HG2 MET sing 243 n n CG HG3 MET sing 244 n n SD CE MET sing 245 n n CE HE1 MET sing 246 n n CE HE2 MET sing 247 n n CE HE3 MET sing 248 n n OXT HXT MET sing 249 n n # _atom_sites.entry_id 5YOH _atom_sites.fract_transf_matrix[1][1] 0.020271 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001881 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020538 _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] 0.017886 _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 CO A 1 301 301 CO CO . C 2 CO A 1 302 302 CO CO . D 3 NA A 1 303 311 NA NA . E 4 MET A 1 304 321 MET MET . F 5 GOL A 1 305 331 GOL GOL . G 6 HOH A 1 401 511 HOH HOH . G 6 HOH A 2 402 420 HOH HOH . G 6 HOH A 3 403 499 HOH HOH . G 6 HOH A 4 404 539 HOH HOH . G 6 HOH A 5 405 458 HOH HOH . G 6 HOH A 6 406 555 HOH HOH . G 6 HOH A 7 407 536 HOH HOH . G 6 HOH A 8 408 396 HOH HOH . G 6 HOH A 9 409 417 HOH HOH . G 6 HOH A 10 410 531 HOH HOH . G 6 HOH A 11 411 520 HOH HOH . G 6 HOH A 12 412 475 HOH HOH . G 6 HOH A 13 413 419 HOH HOH . G 6 HOH A 14 414 477 HOH HOH . G 6 HOH A 15 415 387 HOH HOH . G 6 HOH A 16 416 431 HOH HOH . G 6 HOH A 17 417 464 HOH HOH . G 6 HOH A 18 418 486 HOH HOH . G 6 HOH A 19 419 378 HOH HOH . G 6 HOH A 20 420 421 HOH HOH . G 6 HOH A 21 421 437 HOH HOH . G 6 HOH A 22 422 434 HOH HOH . G 6 HOH A 23 423 393 HOH HOH . G 6 HOH A 24 424 389 HOH HOH . G 6 HOH A 25 425 379 HOH HOH . G 6 HOH A 26 426 530 HOH HOH . G 6 HOH A 27 427 481 HOH HOH . G 6 HOH A 28 428 522 HOH HOH . G 6 HOH A 29 429 351 HOH HOH . G 6 HOH A 30 430 538 HOH HOH . G 6 HOH A 31 431 527 HOH HOH . G 6 HOH A 32 432 553 HOH HOH . G 6 HOH A 33 433 439 HOH HOH . G 6 HOH A 34 434 504 HOH HOH . G 6 HOH A 35 435 517 HOH HOH . G 6 HOH A 36 436 414 HOH HOH . G 6 HOH A 37 437 410 HOH HOH . G 6 HOH A 38 438 484 HOH HOH . G 6 HOH A 39 439 446 HOH HOH . G 6 HOH A 40 440 479 HOH HOH . G 6 HOH A 41 441 505 HOH HOH . G 6 HOH A 42 442 372 HOH HOH . G 6 HOH A 43 443 408 HOH HOH . G 6 HOH A 44 444 471 HOH HOH . G 6 HOH A 45 445 381 HOH HOH . G 6 HOH A 46 446 524 HOH HOH . G 6 HOH A 47 447 485 HOH HOH . G 6 HOH A 48 448 445 HOH HOH . G 6 HOH A 49 449 423 HOH HOH . G 6 HOH A 50 450 367 HOH HOH . G 6 HOH A 51 451 491 HOH HOH . G 6 HOH A 52 452 529 HOH HOH . G 6 HOH A 53 453 430 HOH HOH . G 6 HOH A 54 454 362 HOH HOH . G 6 HOH A 55 455 428 HOH HOH . G 6 HOH A 56 456 494 HOH HOH . G 6 HOH A 57 457 502 HOH HOH . G 6 HOH A 58 458 470 HOH HOH . G 6 HOH A 59 459 397 HOH HOH . G 6 HOH A 60 460 554 HOH HOH . G 6 HOH A 61 461 459 HOH HOH . G 6 HOH A 62 462 535 HOH HOH . G 6 HOH A 63 463 360 HOH HOH . G 6 HOH A 64 464 403 HOH HOH . G 6 HOH A 65 465 497 HOH HOH . G 6 HOH A 66 466 474 HOH HOH . G 6 HOH A 67 467 354 HOH HOH . G 6 HOH A 68 468 433 HOH HOH . G 6 HOH A 69 469 402 HOH HOH . G 6 HOH A 70 470 528 HOH HOH . G 6 HOH A 71 471 472 HOH HOH . G 6 HOH A 72 472 373 HOH HOH . G 6 HOH A 73 473 380 HOH HOH . G 6 HOH A 74 474 540 HOH HOH . G 6 HOH A 75 475 512 HOH HOH . G 6 HOH A 76 476 398 HOH HOH . G 6 HOH A 77 477 549 HOH HOH . G 6 HOH A 78 478 443 HOH HOH . G 6 HOH A 79 479 518 HOH HOH . G 6 HOH A 80 480 355 HOH HOH . G 6 HOH A 81 481 468 HOH HOH . G 6 HOH A 82 482 411 HOH HOH . G 6 HOH A 83 483 438 HOH HOH . G 6 HOH A 84 484 356 HOH HOH . G 6 HOH A 85 485 457 HOH HOH . G 6 HOH A 86 486 432 HOH HOH . G 6 HOH A 87 487 374 HOH HOH . G 6 HOH A 88 488 359 HOH HOH . G 6 HOH A 89 489 363 HOH HOH . G 6 HOH A 90 490 368 HOH HOH . G 6 HOH A 91 491 412 HOH HOH . G 6 HOH A 92 492 467 HOH HOH . G 6 HOH A 93 493 483 HOH HOH . G 6 HOH A 94 494 358 HOH HOH . G 6 HOH A 95 495 476 HOH HOH . G 6 HOH A 96 496 392 HOH HOH . G 6 HOH A 97 497 426 HOH HOH . G 6 HOH A 98 498 422 HOH HOH . G 6 HOH A 99 499 537 HOH HOH . G 6 HOH A 100 500 533 HOH HOH . G 6 HOH A 101 501 407 HOH HOH . G 6 HOH A 102 502 388 HOH HOH . G 6 HOH A 103 503 548 HOH HOH . G 6 HOH A 104 504 541 HOH HOH . G 6 HOH A 105 505 435 HOH HOH . G 6 HOH A 106 506 413 HOH HOH . G 6 HOH A 107 507 371 HOH HOH . G 6 HOH A 108 508 463 HOH HOH . G 6 HOH A 109 509 460 HOH HOH . G 6 HOH A 110 510 384 HOH HOH . G 6 HOH A 111 511 405 HOH HOH . G 6 HOH A 112 512 401 HOH HOH . G 6 HOH A 113 513 404 HOH HOH . G 6 HOH A 114 514 370 HOH HOH . G 6 HOH A 115 515 425 HOH HOH . G 6 HOH A 116 516 465 HOH HOH . G 6 HOH A 117 517 442 HOH HOH . G 6 HOH A 118 518 556 HOH HOH . G 6 HOH A 119 519 365 HOH HOH . G 6 HOH A 120 520 547 HOH HOH . G 6 HOH A 121 521 451 HOH HOH . G 6 HOH A 122 522 532 HOH HOH . G 6 HOH A 123 523 377 HOH HOH . G 6 HOH A 124 524 416 HOH HOH . G 6 HOH A 125 525 488 HOH HOH . G 6 HOH A 126 526 385 HOH HOH . G 6 HOH A 127 527 352 HOH HOH . G 6 HOH A 128 528 493 HOH HOH . G 6 HOH A 129 529 501 HOH HOH . G 6 HOH A 130 530 436 HOH HOH . G 6 HOH A 131 531 543 HOH HOH . G 6 HOH A 132 532 390 HOH HOH . G 6 HOH A 133 533 361 HOH HOH . G 6 HOH A 134 534 375 HOH HOH . G 6 HOH A 135 535 448 HOH HOH . G 6 HOH A 136 536 542 HOH HOH . G 6 HOH A 137 537 400 HOH HOH . G 6 HOH A 138 538 415 HOH HOH . G 6 HOH A 139 539 492 HOH HOH . G 6 HOH A 140 540 523 HOH HOH . G 6 HOH A 141 541 366 HOH HOH . G 6 HOH A 142 542 353 HOH HOH . G 6 HOH A 143 543 461 HOH HOH . G 6 HOH A 144 544 525 HOH HOH . G 6 HOH A 145 545 482 HOH HOH . G 6 HOH A 146 546 495 HOH HOH . G 6 HOH A 147 547 453 HOH HOH . G 6 HOH A 148 548 424 HOH HOH . G 6 HOH A 149 549 440 HOH HOH . G 6 HOH A 150 550 418 HOH HOH . G 6 HOH A 151 551 409 HOH HOH . G 6 HOH A 152 552 382 HOH HOH . G 6 HOH A 153 553 490 HOH HOH . G 6 HOH A 154 554 447 HOH HOH . G 6 HOH A 155 555 466 HOH HOH . G 6 HOH A 156 556 369 HOH HOH . G 6 HOH A 157 557 376 HOH HOH . G 6 HOH A 158 558 452 HOH HOH . G 6 HOH A 159 559 383 HOH HOH . G 6 HOH A 160 560 550 HOH HOH . G 6 HOH A 161 561 427 HOH HOH . G 6 HOH A 162 562 357 HOH HOH . G 6 HOH A 163 563 500 HOH HOH . G 6 HOH A 164 564 514 HOH HOH . G 6 HOH A 165 565 394 HOH HOH . G 6 HOH A 166 566 557 HOH HOH . G 6 HOH A 167 567 480 HOH HOH . G 6 HOH A 168 568 487 HOH HOH . G 6 HOH A 169 569 526 HOH HOH . G 6 HOH A 170 570 364 HOH HOH . G 6 HOH A 171 571 469 HOH HOH . G 6 HOH A 172 572 399 HOH HOH . G 6 HOH A 173 573 395 HOH HOH . G 6 HOH A 174 574 462 HOH HOH . G 6 HOH A 175 575 498 HOH HOH . G 6 HOH A 176 576 441 HOH HOH . G 6 HOH A 177 577 429 HOH HOH . G 6 HOH A 178 578 455 HOH HOH . G 6 HOH A 179 579 386 HOH HOH . G 6 HOH A 180 580 391 HOH HOH . G 6 HOH A 181 581 489 HOH HOH . G 6 HOH A 182 582 473 HOH HOH . G 6 HOH A 183 583 478 HOH HOH . G 6 HOH A 184 584 516 HOH HOH . G 6 HOH A 185 585 503 HOH HOH . G 6 HOH A 186 586 552 HOH HOH . G 6 HOH A 187 587 456 HOH HOH . G 6 HOH A 188 588 521 HOH HOH . G 6 HOH A 189 589 519 HOH HOH . G 6 HOH A 190 590 444 HOH HOH . G 6 HOH A 191 591 551 HOH HOH . G 6 HOH A 192 592 406 HOH HOH . G 6 HOH A 193 593 449 HOH HOH . G 6 HOH A 194 594 496 HOH HOH . G 6 HOH A 195 595 508 HOH HOH . G 6 HOH A 196 596 513 HOH HOH . G 6 HOH A 197 597 507 HOH HOH . G 6 HOH A 198 598 544 HOH HOH . G 6 HOH A 199 599 450 HOH HOH . G 6 HOH A 200 600 454 HOH HOH . G 6 HOH A 201 601 506 HOH HOH . G 6 HOH A 202 602 546 HOH HOH . G 6 HOH A 203 603 545 HOH HOH . G 6 HOH A 204 604 510 HOH HOH . G 6 HOH A 205 605 509 HOH HOH . G 6 HOH A 206 606 515 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 MET . . . E 4 15.64 0.559 8.929 1 19.41 ? N MET 304 A 1 HETATM 2 C CA MET . . . E 4 15.89 -0.952 8.743 1 21.5 ? CA MET 304 A 1 HETATM 3 C C MET . . . E 4 17.274 -1.338 9.261 1 22.89 ? C MET 304 A 1 HETATM 4 O O MET . . . E 4 18.055 -1.947 8.459 1 22.01 ? O MET 304 A 1 HETATM 5 C CB MET . . . E 4 15.692 -1.427 7.255 1 22.67 ? CB MET 304 A 1 HETATM 6 C CG MET . . . E 4 15.695 -2.93 7.021 1 23.59 ? CG MET 304 A 1 HETATM 7 S SD MET . . . E 4 15.878 -3.288 5.267 1 24.71 ? SD MET 304 A 1 HETATM 8 C CE MET . . . E 4 16.149 -5.019 5.303 1 30.66 ? CE MET 304 A 1 HETATM 9 O OXT MET . . . E 4 17.501 -0.879 10.47 1 17.07 ? OXT MET 304 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 9 #