data_5NRB # _model_server_result.job_id 1-bWbhMbx5pl0GgPz4S_Mg _model_server_result.datetime_utc '2025-02-23 22:10:14' _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 5nrb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5NRB # _exptl.entry_id 5NRB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.933 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'COBALT (II) ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.92 _cell.angle_gamma 90 _cell.entry_id 5NRB _cell.length_a 132.963 _cell.length_b 65.646 _cell.length_c 82.654 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NRB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,H 1 1 B,F,G,I 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C BGC 1 C 1 BGC A 361 LAT 2 n C GAL 2 C 2 GAL A 361 LAT # 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 covale ? covale1 C O4 BGC . C BGC 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 sing metalc ? metalc1 A OD2 ASP 149 A ASP 225 1_555 D CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 A OD1 ASP 151 A ASP 227 1_555 D CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc3 D CO CO . A CO 402 1_555 E O1B GDU . A GDU 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc4 D CO CO . A CO 402 1_555 E O1A GDU . A GDU 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 D CO CO . A CO 402 1_555 H O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc6 B OD2 ASP 151 B ASP 227 1_555 F CO CO . B CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc7 F CO CO . B CO 401 1_555 G O1B GDU . B GDU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc8 F CO CO . B CO 401 1_555 G O1A GDU . B GDU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc9 F CO CO . B CO 401 1_555 I O HOH . B HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc10 F CO CO . B CO 401 1_555 I O HOH . B HOH 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? # _chem_comp.formula 'Co 2' _chem_comp.formula_weight 58.933 _chem_comp.id CO _chem_comp.mon_nstd_flag . _chem_comp.name 'COBALT (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5NRB _atom_sites.fract_transf_matrix[1][1] 0.007521 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001725 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015233 _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] 0.012413 _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 D 3 CO A 1 402 362 CO CO . E 4 GDU A 1 403 363 GDU GDU . F 3 CO B 1 401 359 CO CO . G 4 GDU B 1 402 360 GDU GDU . H 5 HOH A 1 501 494 HOH HOH . H 5 HOH A 2 502 409 HOH HOH . H 5 HOH A 3 503 424 HOH HOH . H 5 HOH A 4 504 377 HOH HOH . H 5 HOH A 5 505 460 HOH HOH . H 5 HOH A 6 506 414 HOH HOH . H 5 HOH A 7 507 493 HOH HOH . H 5 HOH A 8 508 389 HOH HOH . H 5 HOH A 9 509 387 HOH HOH . H 5 HOH A 10 510 427 HOH HOH . H 5 HOH A 11 511 405 HOH HOH . H 5 HOH A 12 512 402 HOH HOH . H 5 HOH A 13 513 422 HOH HOH . H 5 HOH A 14 514 390 HOH HOH . H 5 HOH A 15 515 426 HOH HOH . H 5 HOH A 16 516 365 HOH HOH . H 5 HOH A 17 517 384 HOH HOH . H 5 HOH A 18 518 491 HOH HOH . H 5 HOH A 19 519 472 HOH HOH . H 5 HOH A 20 520 466 HOH HOH . H 5 HOH A 21 521 399 HOH HOH . H 5 HOH A 22 522 449 HOH HOH . H 5 HOH A 23 523 430 HOH HOH . H 5 HOH A 24 524 393 HOH HOH . H 5 HOH A 25 525 395 HOH HOH . H 5 HOH A 26 526 462 HOH HOH . H 5 HOH A 27 527 447 HOH HOH . H 5 HOH A 28 528 372 HOH HOH . H 5 HOH A 29 529 441 HOH HOH . H 5 HOH A 30 530 445 HOH HOH . H 5 HOH A 31 531 481 HOH HOH . H 5 HOH A 32 532 436 HOH HOH . H 5 HOH A 33 533 380 HOH HOH . H 5 HOH A 34 534 418 HOH HOH . H 5 HOH A 35 535 381 HOH HOH . H 5 HOH A 36 536 397 HOH HOH . H 5 HOH A 37 537 386 HOH HOH . H 5 HOH A 38 538 464 HOH HOH . H 5 HOH A 39 539 368 HOH HOH . H 5 HOH A 40 540 408 HOH HOH . H 5 HOH A 41 541 423 HOH HOH . H 5 HOH A 42 542 437 HOH HOH . H 5 HOH A 43 543 401 HOH HOH . H 5 HOH A 44 544 446 HOH HOH . H 5 HOH A 45 545 428 HOH HOH . H 5 HOH A 46 546 385 HOH HOH . H 5 HOH A 47 547 394 HOH HOH . H 5 HOH A 48 548 367 HOH HOH . H 5 HOH A 49 549 410 HOH HOH . H 5 HOH A 50 550 374 HOH HOH . H 5 HOH A 51 551 440 HOH HOH . H 5 HOH A 52 552 376 HOH HOH . H 5 HOH A 53 553 448 HOH HOH . H 5 HOH A 54 554 383 HOH HOH . H 5 HOH A 55 555 450 HOH HOH . H 5 HOH A 56 556 416 HOH HOH . H 5 HOH A 57 557 398 HOH HOH . H 5 HOH A 58 558 371 HOH HOH . H 5 HOH A 59 559 453 HOH HOH . H 5 HOH A 60 560 474 HOH HOH . H 5 HOH A 61 561 407 HOH HOH . H 5 HOH A 62 562 382 HOH HOH . H 5 HOH A 63 563 400 HOH HOH . H 5 HOH A 64 564 396 HOH HOH . H 5 HOH A 65 565 433 HOH HOH . H 5 HOH A 66 566 468 HOH HOH . H 5 HOH A 67 567 388 HOH HOH . H 5 HOH A 68 568 370 HOH HOH . H 5 HOH A 69 569 415 HOH HOH . H 5 HOH A 70 570 465 HOH HOH . H 5 HOH A 71 571 366 HOH HOH . H 5 HOH A 72 572 391 HOH HOH . H 5 HOH A 73 573 419 HOH HOH . H 5 HOH A 74 574 483 HOH HOH . H 5 HOH A 75 575 477 HOH HOH . H 5 HOH A 76 576 369 HOH HOH . H 5 HOH A 77 577 467 HOH HOH . H 5 HOH A 78 578 425 HOH HOH . H 5 HOH A 79 579 454 HOH HOH . H 5 HOH A 80 580 412 HOH HOH . H 5 HOH A 81 581 403 HOH HOH . H 5 HOH A 82 582 485 HOH HOH . H 5 HOH A 83 583 373 HOH HOH . H 5 HOH A 84 584 461 HOH HOH . H 5 HOH A 85 585 429 HOH HOH . H 5 HOH A 86 586 457 HOH HOH . H 5 HOH A 87 587 421 HOH HOH . H 5 HOH A 88 588 404 HOH HOH . H 5 HOH A 89 589 392 HOH HOH . H 5 HOH A 90 590 469 HOH HOH . H 5 HOH A 91 591 442 HOH HOH . H 5 HOH A 92 592 444 HOH HOH . H 5 HOH A 93 593 471 HOH HOH . H 5 HOH A 94 594 426 HOH HOH . H 5 HOH A 95 595 406 HOH HOH . H 5 HOH A 96 596 432 HOH HOH . H 5 HOH A 97 597 456 HOH HOH . H 5 HOH A 98 598 379 HOH HOH . H 5 HOH A 99 599 473 HOH HOH . H 5 HOH A 100 600 482 HOH HOH . H 5 HOH A 101 601 489 HOH HOH . H 5 HOH A 102 602 378 HOH HOH . H 5 HOH A 103 603 490 HOH HOH . H 5 HOH A 104 604 479 HOH HOH . H 5 HOH A 105 605 451 HOH HOH . H 5 HOH A 106 606 411 HOH HOH . H 5 HOH A 107 607 476 HOH HOH . H 5 HOH A 108 608 480 HOH HOH . H 5 HOH A 109 609 459 HOH HOH . H 5 HOH A 110 610 434 HOH HOH . H 5 HOH A 111 611 417 HOH HOH . H 5 HOH A 112 612 420 HOH HOH . H 5 HOH A 113 613 413 HOH HOH . H 5 HOH A 114 614 452 HOH HOH . H 5 HOH A 115 615 486 HOH HOH . H 5 HOH A 116 616 438 HOH HOH . H 5 HOH A 117 617 375 HOH HOH . H 5 HOH A 118 618 488 HOH HOH . H 5 HOH A 119 619 478 HOH HOH . H 5 HOH A 120 620 487 HOH HOH . H 5 HOH A 121 621 492 HOH HOH . H 5 HOH A 122 622 475 HOH HOH . H 5 HOH A 123 623 458 HOH HOH . H 5 HOH A 124 624 435 HOH HOH . H 5 HOH A 125 625 463 HOH HOH . H 5 HOH A 126 626 484 HOH HOH . H 5 HOH A 127 627 455 HOH HOH . H 5 HOH A 128 628 443 HOH HOH . H 5 HOH A 129 629 431 HOH HOH . H 5 HOH A 130 630 470 HOH HOH . I 5 HOH B 1 501 397 HOH HOH . I 5 HOH B 2 502 455 HOH HOH . I 5 HOH B 3 503 451 HOH HOH . I 5 HOH B 4 504 385 HOH HOH . I 5 HOH B 5 505 362 HOH HOH . I 5 HOH B 6 506 390 HOH HOH . I 5 HOH B 7 507 377 HOH HOH . I 5 HOH B 8 508 443 HOH HOH . I 5 HOH B 9 509 389 HOH HOH . I 5 HOH B 10 510 371 HOH HOH . I 5 HOH B 11 511 434 HOH HOH . I 5 HOH B 12 512 414 HOH HOH . I 5 HOH B 13 513 384 HOH HOH . I 5 HOH B 14 514 379 HOH HOH . I 5 HOH B 15 515 387 HOH HOH . I 5 HOH B 16 516 375 HOH HOH . I 5 HOH B 17 517 394 HOH HOH . I 5 HOH B 18 518 381 HOH HOH . I 5 HOH B 19 519 412 HOH HOH . I 5 HOH B 20 520 378 HOH HOH . I 5 HOH B 21 521 437 HOH HOH . I 5 HOH B 22 522 399 HOH HOH . I 5 HOH B 23 523 403 HOH HOH . I 5 HOH B 24 524 368 HOH HOH . I 5 HOH B 25 525 417 HOH HOH . I 5 HOH B 26 526 367 HOH HOH . I 5 HOH B 27 527 393 HOH HOH . I 5 HOH B 28 528 435 HOH HOH . I 5 HOH B 29 529 374 HOH HOH . I 5 HOH B 30 530 382 HOH HOH . I 5 HOH B 31 531 364 HOH HOH . I 5 HOH B 32 532 415 HOH HOH . I 5 HOH B 33 533 363 HOH HOH . I 5 HOH B 34 534 423 HOH HOH . I 5 HOH B 35 535 431 HOH HOH . I 5 HOH B 36 536 405 HOH HOH . I 5 HOH B 37 537 407 HOH HOH . I 5 HOH B 38 538 438 HOH HOH . I 5 HOH B 39 539 450 HOH HOH . I 5 HOH B 40 540 391 HOH HOH . I 5 HOH B 41 541 372 HOH HOH . I 5 HOH B 42 542 425 HOH HOH . I 5 HOH B 43 543 383 HOH HOH . I 5 HOH B 44 544 395 HOH HOH . I 5 HOH B 45 545 370 HOH HOH . I 5 HOH B 46 546 386 HOH HOH . I 5 HOH B 47 547 409 HOH HOH . I 5 HOH B 48 548 444 HOH HOH . I 5 HOH B 49 549 401 HOH HOH . I 5 HOH B 50 550 418 HOH HOH . I 5 HOH B 51 551 427 HOH HOH . I 5 HOH B 52 552 419 HOH HOH . I 5 HOH B 53 553 402 HOH HOH . I 5 HOH B 54 554 369 HOH HOH . I 5 HOH B 55 555 373 HOH HOH . I 5 HOH B 56 556 445 HOH HOH . I 5 HOH B 57 557 410 HOH HOH . I 5 HOH B 58 558 422 HOH HOH . I 5 HOH B 59 559 420 HOH HOH . I 5 HOH B 60 560 398 HOH HOH . I 5 HOH B 61 561 428 HOH HOH . I 5 HOH B 62 562 376 HOH HOH . I 5 HOH B 63 563 439 HOH HOH . I 5 HOH B 64 564 441 HOH HOH . I 5 HOH B 65 565 406 HOH HOH . I 5 HOH B 66 566 408 HOH HOH . I 5 HOH B 67 567 366 HOH HOH . I 5 HOH B 68 568 400 HOH HOH . I 5 HOH B 69 569 392 HOH HOH . I 5 HOH B 70 570 365 HOH HOH . I 5 HOH B 71 571 380 HOH HOH . I 5 HOH B 72 572 449 HOH HOH . I 5 HOH B 73 573 430 HOH HOH . I 5 HOH B 74 574 454 HOH HOH . I 5 HOH B 75 575 453 HOH HOH . I 5 HOH B 76 576 416 HOH HOH . I 5 HOH B 77 577 446 HOH HOH . I 5 HOH B 78 578 424 HOH HOH . I 5 HOH B 79 579 411 HOH HOH . I 5 HOH B 80 580 432 HOH HOH . I 5 HOH B 81 581 421 HOH HOH . I 5 HOH B 82 582 388 HOH HOH . I 5 HOH B 83 583 433 HOH HOH . I 5 HOH B 84 584 447 HOH HOH . I 5 HOH B 85 585 404 HOH HOH . I 5 HOH B 86 586 436 HOH HOH . I 5 HOH B 87 587 413 HOH HOH . I 5 HOH B 88 588 442 HOH HOH . I 5 HOH B 89 589 452 HOH HOH . I 5 HOH B 90 590 448 HOH HOH . I 5 HOH B 91 591 396 HOH HOH . I 5 HOH B 92 592 429 HOH HOH . I 5 HOH B 93 593 440 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CO _atom_site.label_atom_id CO _atom_site.label_comp_id CO _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x -20.237 _atom_site.Cartn_y -17.794 _atom_site.Cartn_z 11.318 _atom_site.occupancy 0.51 _atom_site.B_iso_or_equiv 52.31 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CO _atom_site.auth_comp_id CO _atom_site.auth_seq_id 402 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #