data_5NRD # _model_server_result.job_id LU-PRHAtFg9FDzIiTNlssw _model_server_result.datetime_utc '2024-11-25 17:00:30' _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 5nrd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 5NRD # _exptl.entry_id 5NRD _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 102.89 _cell.angle_gamma 90 _cell.entry_id 5NRD _cell.length_a 133.414 _cell.length_b 65.694 _cell.length_c 83.014 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NRD _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,F,I 1 1 B,G,H,J 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 G 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 366 LAT 2 n C GAL 2 C 2 GAL A 366 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 sing metalc ? metalc1 A OD2 ASP 149 A ASP 225 1_555 D CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 A OD1 ASP 151 A ASP 227 1_555 D CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc3 A OD2 ASP 151 A ASP 227 1_555 D CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc4 D CO CO . A CO 402 1_555 E O1B GDU . A GDU 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc5 D CO CO . A CO 402 1_555 E O1A GDU . A GDU 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc6 D CO CO . A CO 402 1_555 I O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc7 B OD2 ASP 151 B ASP 227 1_555 G CO CO . B CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc8 G CO CO . B CO 401 1_555 H O1B GDU . B GDU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc9 G CO CO . B CO 401 1_555 H O1A GDU . B GDU 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc10 G CO CO . B CO 401 1_555 J O HOH . B HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? # _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 5NRD _atom_sites.fract_transf_matrix[1][1] 0.007495 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001716 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015222 _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] 0.012358 _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 1 402 367 CO CO . E 4 GDU A 1 403 368 GDU GDU . F 5 GOL A 1 404 370 GOL GOL . G 3 CO B 1 401 360 CO CO . H 4 GDU B 1 402 361 GDU GDU . I 6 HOH A 1 501 464 HOH HOH . I 6 HOH A 2 502 483 HOH HOH . I 6 HOH A 3 503 388 HOH HOH . I 6 HOH A 4 504 462 HOH HOH . I 6 HOH A 5 505 408 HOH HOH . I 6 HOH A 6 506 371 HOH HOH . I 6 HOH A 7 507 490 HOH HOH . I 6 HOH A 8 508 424 HOH HOH . I 6 HOH A 9 509 378 HOH HOH . I 6 HOH A 10 510 401 HOH HOH . I 6 HOH A 11 511 402 HOH HOH . I 6 HOH A 12 512 419 HOH HOH . I 6 HOH A 13 513 407 HOH HOH . I 6 HOH A 14 514 444 HOH HOH . I 6 HOH A 15 515 403 HOH HOH . I 6 HOH A 16 516 442 HOH HOH . I 6 HOH A 17 517 422 HOH HOH . I 6 HOH A 18 518 446 HOH HOH . I 6 HOH A 19 519 383 HOH HOH . I 6 HOH A 20 520 454 HOH HOH . I 6 HOH A 21 521 382 HOH HOH . I 6 HOH A 22 522 429 HOH HOH . I 6 HOH A 23 523 394 HOH HOH . I 6 HOH A 24 524 385 HOH HOH . I 6 HOH A 25 525 506 HOH HOH . I 6 HOH A 26 526 465 HOH HOH . I 6 HOH A 27 527 489 HOH HOH . I 6 HOH A 28 528 453 HOH HOH . I 6 HOH A 29 529 457 HOH HOH . I 6 HOH A 30 530 499 HOH HOH . I 6 HOH A 31 531 405 HOH HOH . I 6 HOH A 32 532 400 HOH HOH . I 6 HOH A 33 533 466 HOH HOH . I 6 HOH A 34 534 502 HOH HOH . I 6 HOH A 35 535 484 HOH HOH . I 6 HOH A 36 536 503 HOH HOH . I 6 HOH A 37 537 381 HOH HOH . I 6 HOH A 38 538 412 HOH HOH . I 6 HOH A 39 539 477 HOH HOH . I 6 HOH A 40 540 463 HOH HOH . I 6 HOH A 41 541 494 HOH HOH . I 6 HOH A 42 542 439 HOH HOH . I 6 HOH A 43 543 404 HOH HOH . I 6 HOH A 44 544 410 HOH HOH . I 6 HOH A 45 545 443 HOH HOH . I 6 HOH A 46 546 507 HOH HOH . I 6 HOH A 47 547 450 HOH HOH . I 6 HOH A 48 548 445 HOH HOH . I 6 HOH A 49 549 397 HOH HOH . I 6 HOH A 50 550 390 HOH HOH . I 6 HOH A 51 551 421 HOH HOH . I 6 HOH A 52 552 451 HOH HOH . I 6 HOH A 53 553 455 HOH HOH . I 6 HOH A 54 554 426 HOH HOH . I 6 HOH A 55 555 389 HOH HOH . I 6 HOH A 56 556 395 HOH HOH . I 6 HOH A 57 557 379 HOH HOH . I 6 HOH A 58 558 374 HOH HOH . I 6 HOH A 59 559 456 HOH HOH . I 6 HOH A 60 560 468 HOH HOH . I 6 HOH A 61 561 433 HOH HOH . I 6 HOH A 62 562 414 HOH HOH . I 6 HOH A 63 563 467 HOH HOH . I 6 HOH A 64 564 440 HOH HOH . I 6 HOH A 65 565 430 HOH HOH . I 6 HOH A 66 566 417 HOH HOH . I 6 HOH A 67 567 399 HOH HOH . I 6 HOH A 68 568 418 HOH HOH . I 6 HOH A 69 569 461 HOH HOH . I 6 HOH A 70 570 376 HOH HOH . I 6 HOH A 71 571 411 HOH HOH . I 6 HOH A 72 572 372 HOH HOH . I 6 HOH A 73 573 393 HOH HOH . I 6 HOH A 74 574 386 HOH HOH . I 6 HOH A 75 575 482 HOH HOH . I 6 HOH A 76 576 373 HOH HOH . I 6 HOH A 77 577 420 HOH HOH . I 6 HOH A 78 578 496 HOH HOH . I 6 HOH A 79 579 392 HOH HOH . I 6 HOH A 80 580 460 HOH HOH . I 6 HOH A 81 581 472 HOH HOH . I 6 HOH A 82 582 438 HOH HOH . I 6 HOH A 83 583 427 HOH HOH . I 6 HOH A 84 584 387 HOH HOH . I 6 HOH A 85 585 377 HOH HOH . I 6 HOH A 86 586 473 HOH HOH . I 6 HOH A 87 587 458 HOH HOH . I 6 HOH A 88 588 432 HOH HOH . I 6 HOH A 89 589 396 HOH HOH . I 6 HOH A 90 590 428 HOH HOH . I 6 HOH A 91 591 398 HOH HOH . I 6 HOH A 92 592 478 HOH HOH . I 6 HOH A 93 593 416 HOH HOH . I 6 HOH A 94 594 508 HOH HOH . I 6 HOH A 95 595 406 HOH HOH . I 6 HOH A 96 596 459 HOH HOH . I 6 HOH A 97 597 431 HOH HOH . I 6 HOH A 98 598 425 HOH HOH . I 6 HOH A 99 599 448 HOH HOH . I 6 HOH A 100 600 491 HOH HOH . I 6 HOH A 101 601 391 HOH HOH . I 6 HOH A 102 602 505 HOH HOH . I 6 HOH A 103 603 415 HOH HOH . I 6 HOH A 104 604 447 HOH HOH . I 6 HOH A 105 605 384 HOH HOH . I 6 HOH A 106 606 501 HOH HOH . I 6 HOH A 107 607 436 HOH HOH . I 6 HOH A 108 608 452 HOH HOH . I 6 HOH A 109 609 487 HOH HOH . I 6 HOH A 110 610 492 HOH HOH . I 6 HOH A 111 611 380 HOH HOH . I 6 HOH A 112 612 481 HOH HOH . I 6 HOH A 113 613 480 HOH HOH . I 6 HOH A 114 614 470 HOH HOH . I 6 HOH A 115 615 435 HOH HOH . I 6 HOH A 116 616 434 HOH HOH . I 6 HOH A 117 617 476 HOH HOH . I 6 HOH A 118 618 474 HOH HOH . I 6 HOH A 119 619 449 HOH HOH . I 6 HOH A 120 620 437 HOH HOH . I 6 HOH A 121 621 409 HOH HOH . I 6 HOH A 122 622 500 HOH HOH . I 6 HOH A 123 623 488 HOH HOH . I 6 HOH A 124 624 375 HOH HOH . I 6 HOH A 125 625 471 HOH HOH . I 6 HOH A 126 626 475 HOH HOH . I 6 HOH A 127 627 442 HOH HOH . I 6 HOH A 128 628 469 HOH HOH . I 6 HOH A 129 629 385 HOH HOH . I 6 HOH A 130 630 413 HOH HOH . I 6 HOH A 131 631 504 HOH HOH . I 6 HOH A 132 632 479 HOH HOH . I 6 HOH A 133 633 485 HOH HOH . I 6 HOH A 134 634 495 HOH HOH . J 6 HOH B 1 501 382 HOH HOH . J 6 HOH B 2 502 413 HOH HOH . J 6 HOH B 3 503 366 HOH HOH . J 6 HOH B 4 504 381 HOH HOH . J 6 HOH B 5 505 422 HOH HOH . J 6 HOH B 6 506 435 HOH HOH . J 6 HOH B 7 507 420 HOH HOH . J 6 HOH B 8 508 378 HOH HOH . J 6 HOH B 9 509 449 HOH HOH . J 6 HOH B 10 510 423 HOH HOH . J 6 HOH B 11 511 383 HOH HOH . J 6 HOH B 12 512 390 HOH HOH . J 6 HOH B 13 513 429 HOH HOH . J 6 HOH B 14 514 421 HOH HOH . J 6 HOH B 15 515 407 HOH HOH . J 6 HOH B 16 516 380 HOH HOH . J 6 HOH B 17 517 387 HOH HOH . J 6 HOH B 18 518 402 HOH HOH . J 6 HOH B 19 519 399 HOH HOH . J 6 HOH B 20 520 433 HOH HOH . J 6 HOH B 21 521 372 HOH HOH . J 6 HOH B 22 522 373 HOH HOH . J 6 HOH B 23 523 440 HOH HOH . J 6 HOH B 24 524 406 HOH HOH . J 6 HOH B 25 525 369 HOH HOH . J 6 HOH B 26 526 441 HOH HOH . J 6 HOH B 27 527 459 HOH HOH . J 6 HOH B 28 528 403 HOH HOH . J 6 HOH B 29 529 365 HOH HOH . J 6 HOH B 30 530 377 HOH HOH . J 6 HOH B 31 531 370 HOH HOH . J 6 HOH B 32 532 389 HOH HOH . J 6 HOH B 33 533 400 HOH HOH . J 6 HOH B 34 534 394 HOH HOH . J 6 HOH B 35 535 386 HOH HOH . J 6 HOH B 36 536 434 HOH HOH . J 6 HOH B 37 537 439 HOH HOH . J 6 HOH B 38 538 367 HOH HOH . J 6 HOH B 39 539 432 HOH HOH . J 6 HOH B 40 540 411 HOH HOH . J 6 HOH B 41 541 424 HOH HOH . J 6 HOH B 42 542 412 HOH HOH . J 6 HOH B 43 543 431 HOH HOH . J 6 HOH B 44 544 374 HOH HOH . J 6 HOH B 45 545 425 HOH HOH . J 6 HOH B 46 546 404 HOH HOH . J 6 HOH B 47 547 395 HOH HOH . J 6 HOH B 48 548 397 HOH HOH . J 6 HOH B 49 549 388 HOH HOH . J 6 HOH B 50 550 376 HOH HOH . J 6 HOH B 51 551 417 HOH HOH . J 6 HOH B 52 552 392 HOH HOH . J 6 HOH B 53 553 371 HOH HOH . J 6 HOH B 54 554 401 HOH HOH . J 6 HOH B 55 555 426 HOH HOH . J 6 HOH B 56 556 493 HOH HOH . J 6 HOH B 57 557 368 HOH HOH . J 6 HOH B 58 558 398 HOH HOH . J 6 HOH B 59 559 408 HOH HOH . J 6 HOH B 60 560 438 HOH HOH . J 6 HOH B 61 561 384 HOH HOH . J 6 HOH B 62 562 410 HOH HOH . J 6 HOH B 63 563 405 HOH HOH . J 6 HOH B 64 564 423 HOH HOH . J 6 HOH B 65 565 379 HOH HOH . J 6 HOH B 66 566 409 HOH HOH . J 6 HOH B 67 567 391 HOH HOH . J 6 HOH B 68 568 418 HOH HOH . J 6 HOH B 69 569 393 HOH HOH . J 6 HOH B 70 570 414 HOH HOH . J 6 HOH B 71 571 375 HOH HOH . J 6 HOH B 72 572 430 HOH HOH . J 6 HOH B 73 573 447 HOH HOH . J 6 HOH B 74 574 415 HOH HOH . J 6 HOH B 75 575 428 HOH HOH . J 6 HOH B 76 576 436 HOH HOH . J 6 HOH B 77 577 443 HOH HOH . J 6 HOH B 78 578 498 HOH HOH . J 6 HOH B 79 579 448 HOH HOH . J 6 HOH B 80 580 416 HOH HOH . J 6 HOH B 81 581 444 HOH HOH . J 6 HOH B 82 582 437 HOH HOH . J 6 HOH B 83 583 451 HOH HOH . J 6 HOH B 84 584 427 HOH HOH . J 6 HOH B 85 585 445 HOH HOH . J 6 HOH B 86 586 396 HOH HOH . J 6 HOH B 87 587 419 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 G _atom_site.label_entity_id 3 _atom_site.Cartn_x -55.9 _atom_site.Cartn_y -18.069 _atom_site.Cartn_z 23.279 _atom_site.occupancy 0.74 _atom_site.B_iso_or_equiv 58.81 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CO _atom_site.auth_comp_id CO _atom_site.auth_seq_id 401 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #