data_3VRT # _model_server_result.job_id q6hJRPwkpGirn94lAvfntQ _model_server_result.datetime_utc '2025-03-06 09:14:40' _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 3vrt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 3VRT # _exptl.entry_id 3VRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 374.557 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol _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 95.94 _cell.angle_gamma 90 _cell.entry_id 3VRT _cell.length_a 152.988 _cell.length_b 43.867 _cell.length_c 42.428 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _chem_comp.formula 'C24 H38 O3' _chem_comp.formula_weight 374.557 _chem_comp.id YS2 _chem_comp.mon_nstd_flag . _chem_comp.name (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol _chem_comp.type non-polymer _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 C28 C2 YS2 doub 376 n n O1 C1 YS2 sing 377 n n C2 C3 YS2 sing 378 n n C2 C1 YS2 sing 379 n n C3 O2 YS2 sing 380 n n C3 C4 YS2 sing 381 n n C1 C10 YS2 sing 382 n n C4 C5 YS2 sing 383 n n C10 C5 YS2 sing 384 n n C5 C6 YS2 doub 385 n n C6 C7 YS2 sing 386 n n C7 C8 YS2 doub 387 e n C8 C9 YS2 sing 388 n n C8 C14 YS2 sing 389 n n C15 C14 YS2 sing 390 n n C15 C16 YS2 sing 391 n n C18 C13 YS2 sing 392 n n C9 C11 YS2 sing 393 n n C14 C13 YS2 sing 394 n n C16 C17 YS2 sing 395 n n C13 C17 YS2 sing 396 n n C13 C12 YS2 sing 397 n n C24 O3 YS2 sing 398 n n C24 C23 YS2 sing 399 n n C11 C12 YS2 sing 400 n n C17 C20 YS2 sing 401 n n C20 C21 YS2 sing 402 n n C20 C22 YS2 sing 403 n n C23 C22 YS2 sing 404 n n O3 H1 YS2 sing 405 n n C24 H2 YS2 sing 406 n n C24 H3 YS2 sing 407 n n C23 H4 YS2 sing 408 n n C23 H5 YS2 sing 409 n n C22 H6 YS2 sing 410 n n C22 H7 YS2 sing 411 n n C20 H8 YS2 sing 412 n n C21 H9 YS2 sing 413 n n C21 H10 YS2 sing 414 n n C21 H11 YS2 sing 415 n n C17 H12 YS2 sing 416 n n C18 H13 YS2 sing 417 n n C18 H14 YS2 sing 418 n n C18 H15 YS2 sing 419 n n C12 H16 YS2 sing 420 n n C12 H17 YS2 sing 421 n n C11 H18 YS2 sing 422 n n C11 H19 YS2 sing 423 n n C9 H20 YS2 sing 424 n n C9 H21 YS2 sing 425 n n C16 H22 YS2 sing 426 n n C16 H23 YS2 sing 427 n n C15 H24 YS2 sing 428 n n C15 H25 YS2 sing 429 n n C14 H26 YS2 sing 430 n n C7 H27 YS2 sing 431 n n C6 H28 YS2 sing 432 n n C4 H29 YS2 sing 433 n n C4 H30 YS2 sing 434 n n C10 H31 YS2 sing 435 n n C10 H32 YS2 sing 436 n n C1 H33 YS2 sing 437 n n O1 H34 YS2 sing 438 n n C28 H35 YS2 sing 439 n n C28 H36 YS2 sing 440 n n C3 H37 YS2 sing 441 n n O2 H38 YS2 sing 442 n n # _atom_sites.entry_id 3VRT _atom_sites.fract_transf_matrix[1][1] 0.006536 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00068 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022796 _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] 0.023697 _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 C 3 YS2 A 1 501 1 YS2 YS2 . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 2 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 4 HOH HOH . D 4 HOH A 5 605 5 HOH HOH . D 4 HOH A 6 606 6 HOH HOH . D 4 HOH A 7 607 7 HOH HOH . D 4 HOH A 8 608 8 HOH HOH . D 4 HOH A 9 609 11 HOH HOH . D 4 HOH A 10 610 12 HOH HOH . D 4 HOH A 11 611 15 HOH HOH . D 4 HOH A 12 612 17 HOH HOH . D 4 HOH A 13 613 25 HOH HOH . D 4 HOH A 14 614 39 HOH HOH . D 4 HOH A 15 615 45 HOH HOH . D 4 HOH A 16 616 46 HOH HOH . D 4 HOH A 17 617 52 HOH HOH . D 4 HOH A 18 618 55 HOH HOH . D 4 HOH A 19 619 71 HOH HOH . D 4 HOH A 20 620 73 HOH HOH . D 4 HOH A 21 621 74 HOH HOH . D 4 HOH A 22 622 82 HOH HOH . D 4 HOH A 23 623 85 HOH HOH . D 4 HOH A 24 624 91 HOH HOH . D 4 HOH A 25 625 94 HOH HOH . D 4 HOH A 26 626 101 HOH HOH . D 4 HOH A 27 627 102 HOH HOH . D 4 HOH A 28 628 103 HOH HOH . D 4 HOH A 29 629 104 HOH HOH . D 4 HOH A 30 630 107 HOH HOH . D 4 HOH A 31 631 109 HOH HOH . D 4 HOH A 32 632 110 HOH HOH . D 4 HOH A 33 633 112 HOH HOH . D 4 HOH A 34 634 134 HOH HOH . D 4 HOH A 35 635 140 HOH HOH . D 4 HOH A 36 636 141 HOH HOH . D 4 HOH A 37 637 142 HOH HOH . D 4 HOH A 38 638 143 HOH HOH . E 4 HOH C 1 701 83 HOH HOH . E 4 HOH C 2 702 132 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 O3 YS2 . . . C 3 10.515 -5.784 27.387 1 143.7 ? O3 YS2 501 A 1 HETATM 2 C C24 YS2 . . . C 3 11.399 -4.738 26.968 1 122.1 ? C24 YS2 501 A 1 HETATM 3 C C23 YS2 . . . C 3 12.679 -4.792 27.793 1 114.13 ? C23 YS2 501 A 1 HETATM 4 C C22 YS2 . . . C 3 13.056 -3.409 28.309 1 103.02 ? C22 YS2 501 A 1 HETATM 5 C C20 YS2 . . . C 3 12.901 -2.358 27.216 1 86.01 ? C20 YS2 501 A 1 HETATM 6 C C21 YS2 . . . C 3 11.697 -1.463 27.486 1 94.8 ? C21 YS2 501 A 1 HETATM 7 C C17 YS2 . . . C 3 14.171 -1.533 27.069 1 80.77 ? C17 YS2 501 A 1 HETATM 8 C C13 YS2 . . . C 3 13.878 -0.112 26.622 1 73.34 ? C13 YS2 501 A 1 HETATM 9 C C18 YS2 . . . C 3 12.716 -0.128 25.64 1 68.1 ? C18 YS2 501 A 1 HETATM 10 C C12 YS2 . . . C 3 13.622 0.907 27.713 1 83.35 ? C12 YS2 501 A 1 HETATM 11 C C11 YS2 . . . C 3 13.264 2.242 27.051 1 83.34 ? C11 YS2 501 A 1 HETATM 12 C C9 YS2 . . . C 3 14.179 2.679 25.896 1 77.83 ? C9 YS2 501 A 1 HETATM 13 C C16 YS2 . . . C 3 15.104 -2.102 26 1 76.19 ? C16 YS2 501 A 1 HETATM 14 C C15 YS2 . . . C 3 15.578 -0.928 25.14 1 72.23 ? C15 YS2 501 A 1 HETATM 15 C C14 YS2 . . . C 3 15.146 0.3 25.924 1 73.36 ? C14 YS2 501 A 1 HETATM 16 C C8 YS2 . . . C 3 14.79 1.517 25.139 1 69.71 ? C8 YS2 501 A 1 HETATM 17 C C7 YS2 . . . C 3 15.002 1.581 23.818 1 66.6 ? C7 YS2 501 A 1 HETATM 18 C C6 YS2 . . . C 3 14.643 2.787 23.078 1 67.89 ? C6 YS2 501 A 1 HETATM 19 C C5 YS2 . . . C 3 14.222 2.694 21.809 1 65.51 ? C5 YS2 501 A 1 HETATM 20 C C4 YS2 . . . C 3 13.85 3.941 21.043 1 70.79 ? C4 YS2 501 A 1 HETATM 21 C C10 YS2 . . . C 3 14.119 1.342 21.145 1 61.48 ? C10 YS2 501 A 1 HETATM 22 C C1 YS2 . . . C 3 14.855 1.374 19.81 1 64.05 ? C1 YS2 501 A 1 HETATM 23 O O1 YS2 . . . C 3 14.502 0.218 19.043 1 70.27 ? O1 YS2 501 A 1 HETATM 24 C C2 YS2 . . . C 3 14.468 2.612 19.056 1 67.46 ? C2 YS2 501 A 1 HETATM 25 C C28 YS2 . . . C 3 14.022 2.518 17.818 1 70.21 ? C28 YS2 501 A 1 HETATM 26 C C3 YS2 . . . C 3 14.588 3.957 19.71 1 70.6 ? C3 YS2 501 A 1 HETATM 27 O O2 YS2 . . . C 3 15.97 4.258 19.933 1 79.56 ? O2 YS2 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #