data_4EB6 # _model_server_result.job_id MJfHQE5yc14kgqYTswPF8A _model_server_result.datetime_utc '2024-11-23 09:10:37' _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 4eb6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":503}' # _entry.id 4EB6 # _exptl.entry_id 4EB6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 810.974 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE" _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 90 _cell.entry_id 4EB6 _cell.length_a 64.69 _cell.length_b 129.68 _cell.length_c 252.75 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EB6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V _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 8 _struct_asym.id N _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 F O1B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc2 F O2G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc3 G MG MG . A MG 502 1_555 R O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc4 G MG MG . A MG 502 1_555 R O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.051 ? metalc ? metalc5 G MG MG . A MG 502 1_555 R O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc6 G MG MG . A MG 502 1_555 R O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc7 L O1B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc8 L O2G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc9 M MG MG . C MG 502 1_555 T O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc10 M MG MG . C MG 502 1_555 T O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc11 M MG MG . C MG 502 1_555 T O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? # _chem_comp.formula 'C46 H58 N4 O9' _chem_comp.formula_weight 810.974 _chem_comp.id VLB _chem_comp.mon_nstd_flag . _chem_comp.name "(2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms VINBLASTINE # 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 C71 C70 VLB sing 475 n n C71 H711 VLB sing 476 n n C71 H712 VLB sing 477 n n C71 H713 VLB sing 478 n n C70 C54 VLB sing 479 n n C70 H701 VLB sing 480 n n C70 H702 VLB sing 481 n n C54 O72 VLB sing 482 n n C54 C55 VLB sing 483 n n C54 C53 VLB sing 484 n n O72 H72 VLB sing 485 n n C55 N56 VLB sing 486 n n C55 H551 VLB sing 487 n n C55 H552 VLB sing 488 n n C53 C52 VLB sing 489 n n C53 H531 VLB sing 490 n n C53 H532 VLB sing 491 n n C52 C51 VLB sing 492 n n C52 C69 VLB sing 493 n n C52 H52 VLB sing 494 n n C51 C68 VLB sing 495 n n C51 H511 VLB sing 496 n n C51 H512 VLB sing 497 n n C69 N56 VLB sing 498 n n C69 H691 VLB sing 499 n n C69 H692 VLB sing 500 n n N56 C57 VLB sing 501 n n C57 C58 VLB sing 502 n n C57 H571 VLB sing 503 n n C57 H572 VLB sing 504 n n C58 C59 VLB sing 505 n n C58 H581 VLB sing 506 n n C58 H582 VLB sing 507 n n C59 C60 VLB sing 508 n y C59 C67 VLB doub 509 n y C60 C61 VLB doub 510 n y C60 C65 VLB sing 511 n y C61 C62 VLB sing 512 n y C61 H61 VLB sing 513 n n C62 C63 VLB doub 514 n y C62 H62 VLB sing 515 n n C63 C64 VLB sing 516 n y C63 H63 VLB sing 517 n n C64 C65 VLB doub 518 n y C64 H64 VLB sing 519 n n C65 N66 VLB sing 520 n y N66 C67 VLB sing 521 n y N66 H66 VLB sing 522 n n C67 C68 VLB sing 523 n n C68 C73 VLB sing 524 n n C68 C15 VLB sing 525 n n C73 O74 VLB doub 526 n n C73 O75 VLB sing 527 n n O75 C76 VLB sing 528 n n C76 H761 VLB sing 529 n n C76 H762 VLB sing 530 n n C76 H763 VLB sing 531 n n C15 C14 VLB doub 532 n y C15 C16 VLB sing 533 n y C14 C13 VLB sing 534 n y C14 H14 VLB sing 535 n n C13 C12 VLB sing 536 n n C13 C18 VLB doub 537 n y C12 C19 VLB sing 538 n n C12 C11 VLB sing 539 n n C12 C2 VLB sing 540 n n C19 N9 VLB sing 541 n n C19 C5 VLB sing 542 n n C19 H19 VLB sing 543 n n C11 C10 VLB sing 544 n n C11 H111 VLB sing 545 n n C11 H112 VLB sing 546 n n C10 N9 VLB sing 547 n n C10 H101 VLB sing 548 n n C10 H102 VLB sing 549 n n N9 C8 VLB sing 550 n n C8 C7 VLB sing 551 n n C8 H81 VLB sing 552 n n C8 H82 VLB sing 553 n n C7 C6 VLB doub 554 n n C7 H7 VLB sing 555 n n C6 C5 VLB sing 556 n n C6 H6 VLB sing 557 n n C5 C20 VLB sing 558 n n C5 C4 VLB sing 559 n n C20 C21 VLB sing 560 n n C20 H201 VLB sing 561 n n C20 H202 VLB sing 562 n n C21 H211 VLB sing 563 n n C21 H212 VLB sing 564 n n C21 H213 VLB sing 565 n n C4 O28 VLB sing 566 n n C4 C3 VLB sing 567 n n C4 H4 VLB sing 568 n n O28 C29 VLB sing 569 n n C29 C30 VLB sing 570 n n C29 O31 VLB doub 571 n n C30 H301 VLB sing 572 n n C30 H302 VLB sing 573 n n C30 H303 VLB sing 574 n n C3 C23 VLB sing 575 n n C3 O27 VLB sing 576 n n C3 C2 VLB sing 577 n n C23 O24 VLB doub 578 n n C23 O25 VLB sing 579 n n O25 C26 VLB sing 580 n n C26 H261 VLB sing 581 n n C26 H262 VLB sing 582 n n C26 H263 VLB sing 583 n n O27 H27 VLB sing 584 n n C2 N1 VLB sing 585 n n C2 H2 VLB sing 586 n n N1 C22 VLB sing 587 n n N1 C18 VLB sing 588 n n C22 H221 VLB sing 589 n n C22 H222 VLB sing 590 n n C22 H223 VLB sing 591 n n C18 C17 VLB sing 592 n y C17 C16 VLB doub 593 n y C17 H17 VLB sing 594 n n C16 O32 VLB sing 595 n n O32 C33 VLB sing 596 n n C33 H331 VLB sing 597 n n C33 H332 VLB sing 598 n n C33 H333 VLB sing 599 n n # _atom_sites.entry_id 4EB6 _atom_sites.fract_transf_matrix[1][1] 0.015458 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007711 _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] 0.003956 _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 F 4 GTP A 1 501 501 GTP GTP . G 5 MG A 1 502 502 MG MG . H 6 SO4 A 1 503 503 SO4 SO4 . I 6 SO4 A 1 504 504 SO4 SO4 . J 7 GDP B 1 501 501 GDP GDP . K 6 SO4 B 1 502 502 SO4 SO4 . L 4 GTP C 1 501 501 GTP GTP . M 5 MG C 1 502 502 MG MG . N 8 VLB C 1 503 503 VLB VLB . O 7 GDP D 1 501 501 GDP GDP . P 6 SO4 D 1 502 502 SO4 SO4 . Q 6 SO4 D 1 503 503 SO4 SO4 . R 9 HOH A 1 601 601 HOH HOH . R 9 HOH A 2 602 602 HOH HOH . R 9 HOH A 3 603 603 HOH HOH . R 9 HOH A 4 604 604 HOH HOH . R 9 HOH A 5 605 605 HOH HOH . S 9 HOH B 1 601 601 HOH HOH . S 9 HOH B 2 602 602 HOH HOH . S 9 HOH B 3 603 603 HOH HOH . T 9 HOH C 1 601 601 HOH HOH . T 9 HOH C 2 602 602 HOH HOH . T 9 HOH C 3 603 603 HOH HOH . T 9 HOH C 4 604 604 HOH HOH . T 9 HOH C 5 605 605 HOH HOH . T 9 HOH C 6 606 606 HOH HOH . T 9 HOH C 7 607 607 HOH HOH . T 9 HOH C 8 608 608 HOH HOH . T 9 HOH C 9 609 609 HOH HOH . T 9 HOH C 10 610 610 HOH HOH . T 9 HOH C 11 611 611 HOH HOH . T 9 HOH C 12 612 612 HOH HOH . T 9 HOH C 13 613 613 HOH HOH . U 9 HOH D 1 601 601 HOH HOH . U 9 HOH D 2 602 602 HOH HOH . U 9 HOH D 3 603 603 HOH HOH . U 9 HOH D 4 604 604 HOH HOH . U 9 HOH D 5 605 605 HOH HOH . U 9 HOH D 6 606 606 HOH HOH . U 9 HOH D 7 607 607 HOH HOH . U 9 HOH D 8 608 608 HOH HOH . U 9 HOH D 9 609 609 HOH HOH . V 9 HOH E 1 201 201 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 C C71 VLB . . . N 8 9.438 88.406 100.332 1 159.22 ? C71 VLB 503 C 1 HETATM 2 C C70 VLB . . . N 8 10.037 87.071 100.828 1 159.22 ? C70 VLB 503 C 1 HETATM 3 C C54 VLB . . . N 8 11.251 87.104 101.794 1 159.04 ? C54 VLB 503 C 1 HETATM 4 O O72 VLB . . . N 8 12.09 85.986 101.529 1 158.77 ? O72 VLB 503 C 1 HETATM 5 C C55 VLB . . . N 8 12.145 88.36 101.607 1 159.23 ? C55 VLB 503 C 1 HETATM 6 C C53 VLB . . . N 8 10.733 86.876 103.233 1 159.07 ? C53 VLB 503 C 1 HETATM 7 C C52 VLB . . . N 8 10.916 88.074 104.176 1 159.33 ? C52 VLB 503 C 1 HETATM 8 C C51 VLB . . . N 8 12.324 87.978 104.858 1 159.16 ? C51 VLB 503 C 1 HETATM 9 C C69 VLB . . . N 8 10.614 89.345 103.343 1 159.42 ? C69 VLB 503 C 1 HETATM 10 N N56 VLB . . . N 8 11.58 89.571 102.23 1 159.52 ? N56 VLB 503 C 1 HETATM 11 C C57 VLB . . . N 8 12.595 90.646 102.419 1 160.06 ? C57 VLB 503 C 1 HETATM 12 C C58 VLB . . . N 8 13.391 90.61 103.739 1 160.44 ? C58 VLB 503 C 1 HETATM 13 C C59 VLB . . . N 8 12.526 91.034 104.949 1 160.52 ? C59 VLB 503 C 1 HETATM 14 C C60 VLB . . . N 8 11.996 92.304 105.103 1 160.79 ? C60 VLB 503 C 1 HETATM 15 C C61 VLB . . . N 8 12.083 93.468 104.305 1 160.67 ? C61 VLB 503 C 1 HETATM 16 C C62 VLB . . . N 8 11.427 94.631 104.722 1 160.42 ? C62 VLB 503 C 1 HETATM 17 C C63 VLB . . . N 8 10.705 94.633 105.934 1 160.18 ? C63 VLB 503 C 1 HETATM 18 C C64 VLB . . . N 8 10.627 93.469 106.729 1 160.1 ? C64 VLB 503 C 1 HETATM 19 C C65 VLB . . . N 8 11.275 92.296 106.311 1 160.45 ? C65 VLB 503 C 1 HETATM 20 N N66 VLB . . . N 8 11.367 91.073 106.843 1 160.26 ? N66 VLB 503 C 1 HETATM 21 C C67 VLB . . . N 8 12.097 90.259 106.058 1 159.8 ? C67 VLB 503 C 1 HETATM 22 C C68 VLB . . . N 8 12.532 88.758 106.192 1 158.62 ? C68 VLB 503 C 1 HETATM 23 C C73 VLB . . . N 8 14.024 88.917 106.595 1 158.9 ? C73 VLB 503 C 1 HETATM 24 O O74 VLB . . . N 8 14.28 89.563 107.627 1 159.67 ? O74 VLB 503 C 1 HETATM 25 O O75 VLB . . . N 8 15.044 88.35 105.863 1 158.39 ? O75 VLB 503 C 1 HETATM 26 C C76 VLB . . . N 8 16.125 87.897 106.705 1 158.03 ? C76 VLB 503 C 1 HETATM 27 C C15 VLB . . . N 8 11.761 87.893 107.248 1 156.73 ? C15 VLB 503 C 1 HETATM 28 C C14 VLB . . . N 8 10.387 88.127 107.432 1 156.7 ? C14 VLB 503 C 1 HETATM 29 C C13 VLB . . . N 8 9.638 87.378 108.338 1 157.05 ? C13 VLB 503 C 1 HETATM 30 C C12 VLB . . . N 8 8.192 87.478 108.692 1 159.15 ? C12 VLB 503 C 1 HETATM 31 C C19 VLB . . . N 8 8.03 88.843 109.399 1 160.94 ? C19 VLB 503 C 1 HETATM 32 C C11 VLB . . . N 8 7.36 87.555 107.414 1 159.51 ? C11 VLB 503 C 1 HETATM 33 C C10 VLB . . . N 8 6.327 88.652 107.678 1 160.33 ? C10 VLB 503 C 1 HETATM 34 N N9 VLB . . . N 8 6.827 89.501 108.782 1 160.88 ? N9 VLB 503 C 1 HETATM 35 C C8 VLB . . . N 8 5.73 89.822 109.733 1 160.93 ? C8 VLB 503 C 1 HETATM 36 C C7 VLB . . . N 8 6.242 90.459 110.862 1 161.22 ? C7 VLB 503 C 1 HETATM 37 C C6 VLB . . . N 8 7.414 89.972 111.466 1 161.82 ? C6 VLB 503 C 1 HETATM 38 C C5 VLB . . . N 8 8.094 88.831 110.977 1 162.3 ? C5 VLB 503 C 1 HETATM 39 C C20 VLB . . . N 8 9.559 89.052 111.429 1 162.15 ? C20 VLB 503 C 1 HETATM 40 C C21 VLB . . . N 8 10.309 87.9 112.123 1 161.9 ? C21 VLB 503 C 1 HETATM 41 C C4 VLB . . . N 8 7.464 87.522 111.625 1 163.77 ? C4 VLB 503 C 1 HETATM 42 O O28 VLB . . . N 8 6.433 87.805 112.627 1 166.91 ? O28 VLB 503 C 1 HETATM 43 C C29 VLB . . . N 8 6.853 87.765 113.946 1 169.14 ? C29 VLB 503 C 1 HETATM 44 C C30 VLB . . . N 8 8.026 88.391 114.407 1 169.18 ? C30 VLB 503 C 1 HETATM 45 O O31 VLB . . . N 8 6.138 87.18 114.769 1 170.36 ? O31 VLB 503 C 1 HETATM 46 C C3 VLB . . . N 8 6.963 86.397 110.669 1 161.51 ? C3 VLB 503 C 1 HETATM 47 C C23 VLB . . . N 8 6.787 85.062 111.425 1 160.53 ? C23 VLB 503 C 1 HETATM 48 O O24 VLB . . . N 8 5.838 84.297 111.167 1 160.14 ? O24 VLB 503 C 1 HETATM 49 O O25 VLB . . . N 8 7.744 84.702 112.335 1 160.13 ? O25 VLB 503 C 1 HETATM 50 C C26 VLB . . . N 8 7.204 84.403 113.63 1 160.19 ? C26 VLB 503 C 1 HETATM 51 O O27 VLB . . . N 8 5.676 86.748 110.128 1 162 ? O27 VLB 503 C 1 HETATM 52 C C2 VLB . . . N 8 7.955 86.206 109.496 1 159.23 ? C2 VLB 503 C 1 HETATM 53 N N1 VLB . . . N 8 9.309 85.773 109.914 1 157.01 ? N1 VLB 503 C 1 HETATM 54 C C22 VLB . . . N 8 9.416 84.318 109.724 1 156.67 ? C22 VLB 503 C 1 HETATM 55 C C18 VLB . . . N 8 10.208 86.359 109.11 1 156.04 ? C18 VLB 503 C 1 HETATM 56 C C17 VLB . . . N 8 11.57 86.104 108.943 1 155.1 ? C17 VLB 503 C 1 HETATM 57 C C16 VLB . . . N 8 12.342 86.833 108.033 1 155.16 ? C16 VLB 503 C 1 HETATM 58 O O32 VLB . . . N 8 13.633 86.455 107.977 1 154.39 ? O32 VLB 503 C 1 HETATM 59 C C33 VLB . . . N 8 13.784 85.54 106.891 1 154.54 ? C33 VLB 503 C 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 59 #