data_3VRM # _model_server_result.job_id ox421PsBoBitu6CvPjpy0A _model_server_result.datetime_utc '2024-11-18 00:43:10' _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 3vrm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 3VRM # _exptl.entry_id 3VRM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.638 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL' _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 3VRM _cell.length_a 61.421 _cell.length_b 105.521 _cell.length_c 141.988 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VRM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 347 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 347 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 2.378 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C27 H44 O' _chem_comp.formula_weight 384.638 _chem_comp.id VD3 _chem_comp.mon_nstd_flag . _chem_comp.name '(1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN D3' # 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 O C3 VD3 sing 458 n n O HO VD3 sing 459 n n C1 C2 VD3 sing 460 n n C1 C6 VD3 sing 461 n n C1 H11 VD3 sing 462 n n C1 H12 VD3 sing 463 n n C2 C3 VD3 sing 464 n n C2 H21 VD3 sing 465 n n C2 H22 VD3 sing 466 n n C3 C4 VD3 sing 467 n n C3 H3 VD3 sing 468 n n C4 C5 VD3 sing 469 n n C4 H41 VD3 sing 470 n n C4 H42 VD3 sing 471 n n C5 C7 VD3 doub 472 e n C5 C6 VD3 sing 473 n n C7 C8 VD3 sing 474 n n C7 H7 VD3 sing 475 n n C8 C9 VD3 doub 476 z n C8 H8 VD3 sing 477 n n C9 C10 VD3 sing 478 n n C9 C14 VD3 sing 479 n n C10 C11 VD3 sing 480 n n C10 H101 VD3 sing 481 n n C10 H102 VD3 sing 482 n n C6 C19 VD3 doub 483 n n C11 C12 VD3 sing 484 n n C11 H111 VD3 sing 485 n n C11 H112 VD3 sing 486 n n C12 C13 VD3 sing 487 n n C12 H121 VD3 sing 488 n n C12 H122 VD3 sing 489 n n C13 C14 VD3 sing 490 n n C13 C17 VD3 sing 491 n n C13 C18 VD3 sing 492 n n C14 C15 VD3 sing 493 n n C14 H14 VD3 sing 494 n n C15 C16 VD3 sing 495 n n C15 H151 VD3 sing 496 n n C15 H152 VD3 sing 497 n n C16 C17 VD3 sing 498 n n C16 H161 VD3 sing 499 n n C16 H162 VD3 sing 500 n n C17 C20 VD3 sing 501 n n C17 H17 VD3 sing 502 n n C18 H181 VD3 sing 503 n n C18 H182 VD3 sing 504 n n C18 H183 VD3 sing 505 n n C19 H191 VD3 sing 506 n n C19 H192 VD3 sing 507 n n C20 C21 VD3 sing 508 n n C20 C22 VD3 sing 509 n n C20 H20 VD3 sing 510 n n C21 H211 VD3 sing 511 n n C21 H212 VD3 sing 512 n n C21 H213 VD3 sing 513 n n C22 C23 VD3 sing 514 n n C22 H221 VD3 sing 515 n n C22 H222 VD3 sing 516 n n C23 C24 VD3 sing 517 n n C23 H231 VD3 sing 518 n n C23 H232 VD3 sing 519 n n C24 C25 VD3 sing 520 n n C24 H241 VD3 sing 521 n n C24 H242 VD3 sing 522 n n C25 C26 VD3 sing 523 n n C25 C27 VD3 sing 524 n n C25 H25 VD3 sing 525 n n C26 H261 VD3 sing 526 n n C26 H262 VD3 sing 527 n n C26 H263 VD3 sing 528 n n C27 H271 VD3 sing 529 n n C27 H272 VD3 sing 530 n n C27 H273 VD3 sing 531 n n # _atom_sites.entry_id 3VRM _atom_sites.fract_transf_matrix[1][1] 0.016281 _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] 0.009477 _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] 0.007043 _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 HEM A 1 501 411 HEM HEM . C 3 VD3 A 1 502 421 VD3 VD3 . D 4 HOH A 1 601 501 HOH HOH . D 4 HOH A 2 602 502 HOH HOH . D 4 HOH A 3 603 503 HOH HOH . D 4 HOH A 4 604 504 HOH HOH . D 4 HOH A 5 605 505 HOH HOH . D 4 HOH A 6 606 506 HOH HOH . D 4 HOH A 7 607 507 HOH HOH . D 4 HOH A 8 608 508 HOH HOH . D 4 HOH A 9 609 509 HOH HOH . D 4 HOH A 10 610 510 HOH HOH . D 4 HOH A 11 611 511 HOH HOH . D 4 HOH A 12 612 512 HOH HOH . D 4 HOH A 13 613 513 HOH HOH . D 4 HOH A 14 614 514 HOH HOH . D 4 HOH A 15 615 515 HOH HOH . D 4 HOH A 16 616 516 HOH HOH . D 4 HOH A 17 617 517 HOH HOH . D 4 HOH A 18 618 518 HOH HOH . D 4 HOH A 19 619 519 HOH HOH . D 4 HOH A 20 620 520 HOH HOH . D 4 HOH A 21 621 521 HOH HOH . D 4 HOH A 22 622 522 HOH HOH . D 4 HOH A 23 623 523 HOH HOH . D 4 HOH A 24 624 524 HOH HOH . D 4 HOH A 25 625 525 HOH HOH . D 4 HOH A 26 626 526 HOH HOH . D 4 HOH A 27 627 527 HOH HOH . D 4 HOH A 28 628 528 HOH HOH . D 4 HOH A 29 629 529 HOH HOH . D 4 HOH A 30 630 530 HOH HOH . D 4 HOH A 31 631 531 HOH HOH . D 4 HOH A 32 632 532 HOH HOH . D 4 HOH A 33 633 533 HOH HOH . D 4 HOH A 34 634 534 HOH HOH . D 4 HOH A 35 635 535 HOH HOH . D 4 HOH A 36 636 536 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 O O VD3 . A . C 3 -0.287 9.696 18.737 0.5 67.72 ? O VD3 502 A 1 HETATM 2 O O VD3 . B . C 3 -1.346 13.492 21.459 0.5 60.1 ? O VD3 502 A 1 HETATM 3 C C1 VD3 . A . C 3 2.527 11.288 16.821 0.5 65.81 ? C1 VD3 502 A 1 HETATM 4 C C1 VD3 . B . C 3 -1.899 16.09 20.345 0.5 63.87 ? C1 VD3 502 A 1 HETATM 5 C C2 VD3 . A . C 3 1.228 10.529 17.062 0.5 68.14 ? C2 VD3 502 A 1 HETATM 6 C C2 VD3 . B . C 3 -3.001 15.074 20.645 0.5 65.29 ? C2 VD3 502 A 1 HETATM 7 C C3 VD3 . A . C 3 0.848 10.546 18.538 0.5 67.99 ? C3 VD3 502 A 1 HETATM 8 C C3 VD3 . B . C 3 -2.491 13.632 20.605 0.5 65.73 ? C3 VD3 502 A 1 HETATM 9 C C4 VD3 . A . C 3 0.484 11.96 18.976 0.5 68.75 ? C4 VD3 502 A 1 HETATM 10 C C4 VD3 . B . C 3 -2.055 13.322 19.183 0.5 67.96 ? C4 VD3 502 A 1 HETATM 11 C C5 VD3 . A . C 3 1.436 13 18.415 0.5 68.16 ? C5 VD3 502 A 1 HETATM 12 C C5 VD3 . B . C 3 -0.893 14.245 18.898 0.5 67.5 ? C5 VD3 502 A 1 HETATM 13 C C7 VD3 . A . C 3 1.442 14.238 18.928 0.5 69.03 ? C7 VD3 502 A 1 HETATM 14 C C7 VD3 . B . C 3 -0.105 14.004 17.84 0.5 66.34 ? C7 VD3 502 A 1 HETATM 15 C C8 VD3 . A . C 3 2.374 15.186 18.331 0.5 68.88 ? C8 VD3 502 A 1 HETATM 16 C C8 VD3 . B . C 3 1.034 14.838 17.465 0.5 70.22 ? C8 VD3 502 A 1 HETATM 17 C C9 VD3 . A . C 3 1.91 16.332 17.813 0.5 67.26 ? C9 VD3 502 A 1 HETATM 18 C C9 VD3 . B . C 3 0.82 16.124 17.143 0.5 70.08 ? C9 VD3 502 A 1 HETATM 19 C C10 VD3 . A . C 3 0.427 16.652 17.827 0.5 65.03 ? C10 VD3 502 A 1 HETATM 20 C C10 VD3 . B . C 3 -0.591 16.67 17.166 0.5 68.99 ? C10 VD3 502 A 1 HETATM 21 C C6 VD3 . A . C 3 2.37 12.702 17.326 0.5 65.94 ? C6 VD3 502 A 1 HETATM 22 C C6 VD3 . B . C 3 -0.684 15.367 19.815 0.5 66.68 ? C6 VD3 502 A 1 HETATM 23 C C11 VD3 . A . C 3 0.11 18.14 17.635 0.5 65.43 ? C11 VD3 502 A 1 HETATM 24 C C11 VD3 . B . C 3 -0.637 18.178 17.425 0.5 69.77 ? C11 VD3 502 A 1 HETATM 25 C C12 VD3 . A . C 3 1.089 18.91 16.746 0.5 64.78 ? C12 VD3 502 A 1 HETATM 26 C C12 VD3 . B . C 3 0.435 18.971 16.678 0.5 69.59 ? C12 VD3 502 A 1 HETATM 27 C C13 VD3 . A . C 3 2.484 18.727 17.306 0.5 64.54 ? C13 VD3 502 A 1 HETATM 28 C C13 VD3 . B . C 3 1.783 18.46 17.142 0.5 69.89 ? C13 VD3 502 A 1 HETATM 29 C C14 VD3 . A . C 3 2.871 17.276 17.16 0.5 67.56 ? C14 VD3 502 A 1 HETATM 30 C C14 VD3 . B . C 3 1.944 17.022 16.699 0.5 70.61 ? C14 VD3 502 A 1 HETATM 31 C C15 VD3 . A . C 3 4.315 17.232 17.636 0.5 67.58 ? C15 VD3 502 A 1 HETATM 32 C C15 VD3 . B . C 3 3.373 16.677 17.106 0.5 71.26 ? C15 VD3 502 A 1 HETATM 33 C C16 VD3 . A . C 3 4.857 18.562 17.092 0.5 66.72 ? C16 VD3 502 A 1 HETATM 34 C C16 VD3 . B . C 3 4.101 18.007 16.84 0.5 71.41 ? C16 VD3 502 A 1 HETATM 35 C C17 VD3 . A . C 3 3.651 19.336 16.55 0.5 64.92 ? C17 VD3 502 A 1 HETATM 36 C C17 VD3 . B . C 3 3.024 19.047 16.506 0.5 69.17 ? C17 VD3 502 A 1 HETATM 37 C C18 VD3 . A . C 3 2.537 19.151 18.766 0.5 59.7 ? C18 VD3 502 A 1 HETATM 38 C C18 VD3 . B . C 3 1.915 18.605 18.653 0.5 67.7 ? C18 VD3 502 A 1 HETATM 39 C C19 VD3 . A . C 3 3.092 13.674 16.793 0.5 60.73 ? C19 VD3 502 A 1 HETATM 40 C C19 VD3 . B . C 3 0.528 15.735 20.194 0.5 64.26 ? C19 VD3 502 A 1 HETATM 41 C C20 VD3 . A . C 3 3.794 20.847 16.657 0.5 66.23 ? C20 VD3 502 A 1 HETATM 42 C C20 VD3 . B . C 3 3.332 20.466 16.962 0.5 70.44 ? C20 VD3 502 A 1 HETATM 43 C C21 VD3 . A . C 3 2.544 21.523 16.115 0.5 65.5 ? C21 VD3 502 A 1 HETATM 44 C C21 VD3 . B . C 3 2.692 21.466 16.008 0.5 68.56 ? C21 VD3 502 A 1 HETATM 45 C C22 VD3 . A . C 3 5.023 21.309 15.883 0.5 64.89 ? C22 VD3 502 A 1 HETATM 46 C C22 VD3 . B . C 3 4.831 20.719 17.045 0.5 68.64 ? C22 VD3 502 A 1 HETATM 47 C C23 VD3 . A . C 3 5.866 22.298 16.681 0.5 66.46 ? C23 VD3 502 A 1 HETATM 48 C C23 VD3 . B . C 3 5.312 21.542 15.855 0.5 66.53 ? C23 VD3 502 A 1 HETATM 49 C C24 VD3 . A . C 3 7.328 21.859 16.764 0.5 65.68 ? C24 VD3 502 A 1 HETATM 50 C C24 VD3 . B . C 3 6.65 22.206 16.165 0.5 66.83 ? C24 VD3 502 A 1 HETATM 51 C C25 VD3 . A . C 3 7.989 21.87 15.391 0.5 64.26 ? C25 VD3 502 A 1 HETATM 52 C C25 VD3 . B . C 3 7.675 21.936 15.073 0.5 64.82 ? C25 VD3 502 A 1 HETATM 53 C C26 VD3 . A . C 3 7.937 23.266 14.794 0.5 64 ? C26 VD3 502 A 1 HETATM 54 C C26 VD3 . B . C 3 7.832 23.166 14.197 0.5 65.32 ? C26 VD3 502 A 1 HETATM 55 C C27 VD3 . A . C 3 9.426 21.364 15.446 0.5 62.5 ? C27 VD3 502 A 1 HETATM 56 C C27 VD3 . B . C 3 9.024 21.53 15.655 0.5 64.16 ? C27 VD3 502 A 1 # _model_server_stats.io_time_ms 123 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 370 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 56 #