data_8VCD # _model_server_result.job_id tUjCAI-18-SaB0yitzvIAw _model_server_result.datetime_utc '2024-10-12 21:16:37' _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 8vcd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 8VCD # _exptl.entry_id 8VCD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 114.099 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-5-hydroxy-3-methylfuran-2(5H)-one _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 8VCD _cell.length_a 84.34 _cell.length_b 84.34 _cell.length_c 117.44 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 169 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 169 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id C06 _struct_conn.ptnr2_label_comp_id VTY _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id VTY _struct_conn.ptnr2_auth_seq_id 403 _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 1.376 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C5 H6 O3' _chem_comp.formula_weight 114.099 _chem_comp.id VTY _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-5-hydroxy-3-methylfuran-2(5H)-one _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 O08 C04 VTY sing 389 n n C04 C03 VTY sing 390 n n C04 O05 VTY sing 391 n n C03 C02 VTY doub 392 n n O05 C06 VTY sing 393 n n C06 C02 VTY sing 394 n n C06 O07 VTY doub 395 n n C02 C01 VTY sing 396 n n C01 H012 VTY sing 397 n n C01 H013 VTY sing 398 n n C01 H011 VTY sing 399 n n C03 H031 VTY sing 400 n n C04 H041 VTY sing 401 n n O08 H081 VTY sing 402 n n # _atom_sites.entry_id 8VCD _atom_sites.fract_transf_matrix[1][1] 0.011857 _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] 0.011857 _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] 0.008515 _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 GOL A 1 401 401 GOL GOL . C 2 GOL A 1 402 403 GOL GOL . D 3 VTY A 1 403 400 VTY VTY . E 4 HOH A 1 501 547 HOH HOH . E 4 HOH A 2 502 597 HOH HOH . E 4 HOH A 3 503 541 HOH HOH . E 4 HOH A 4 504 543 HOH HOH . E 4 HOH A 5 505 525 HOH HOH . E 4 HOH A 6 506 522 HOH HOH . E 4 HOH A 7 507 567 HOH HOH . E 4 HOH A 8 508 554 HOH HOH . E 4 HOH A 9 509 507 HOH HOH . E 4 HOH A 10 510 520 HOH HOH . E 4 HOH A 11 511 545 HOH HOH . E 4 HOH A 12 512 514 HOH HOH . E 4 HOH A 13 513 523 HOH HOH . E 4 HOH A 14 514 539 HOH HOH . E 4 HOH A 15 515 602 HOH HOH . E 4 HOH A 16 516 560 HOH HOH . E 4 HOH A 17 517 540 HOH HOH . E 4 HOH A 18 518 511 HOH HOH . E 4 HOH A 19 519 504 HOH HOH . E 4 HOH A 20 520 556 HOH HOH . E 4 HOH A 21 521 549 HOH HOH . E 4 HOH A 22 522 546 HOH HOH . E 4 HOH A 23 523 553 HOH HOH . E 4 HOH A 24 524 562 HOH HOH . E 4 HOH A 25 525 502 HOH HOH . E 4 HOH A 26 526 501 HOH HOH . E 4 HOH A 27 527 509 HOH HOH . E 4 HOH A 28 528 506 HOH HOH . E 4 HOH A 29 529 503 HOH HOH . E 4 HOH A 30 530 516 HOH HOH . E 4 HOH A 31 531 531 HOH HOH . E 4 HOH A 32 532 544 HOH HOH . E 4 HOH A 33 533 595 HOH HOH . E 4 HOH A 34 534 557 HOH HOH . E 4 HOH A 35 535 515 HOH HOH . E 4 HOH A 36 536 521 HOH HOH . E 4 HOH A 37 537 598 HOH HOH . E 4 HOH A 38 538 551 HOH HOH . E 4 HOH A 39 539 530 HOH HOH . E 4 HOH A 40 540 573 HOH HOH . E 4 HOH A 41 541 579 HOH HOH . E 4 HOH A 42 542 529 HOH HOH . E 4 HOH A 43 543 576 HOH HOH . E 4 HOH A 44 544 534 HOH HOH . E 4 HOH A 45 545 538 HOH HOH . E 4 HOH A 46 546 536 HOH HOH . E 4 HOH A 47 547 518 HOH HOH . E 4 HOH A 48 548 593 HOH HOH . E 4 HOH A 49 549 599 HOH HOH . E 4 HOH A 50 550 566 HOH HOH . E 4 HOH A 51 551 592 HOH HOH . E 4 HOH A 52 552 601 HOH HOH . E 4 HOH A 53 553 535 HOH HOH . E 4 HOH A 54 554 563 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 C01 VTY . . . D 3 9.495 11.394 9.464 1 53.87 ? C01 VTY 403 A 1 HETATM 2 C C02 VTY . . . D 3 8.371 10.77 10.291 1 58.83 ? C02 VTY 403 A 1 HETATM 3 C C03 VTY . . . D 3 7.108 11.168 10.331 1 66.5 ? C03 VTY 403 A 1 HETATM 4 C C04 VTY . . . D 3 6.573 10.793 11.704 1 59.3 ? C04 VTY 403 A 1 HETATM 5 C C06 VTY . . . D 3 8.54 9.724 11.414 1 48.47 ? C06 VTY 403 A 1 HETATM 6 O O05 VTY . . . D 3 7.437 9.857 12.278 1 66.57 ? O05 VTY 403 A 1 HETATM 7 O O07 VTY . . . D 3 9.426 8.942 11.529 1 69.31 ? O07 VTY 403 A 1 HETATM 8 O O08 VTY . . . D 3 5.295 10.215 11.598 1 74.93 ? O08 VTY 403 A 1 HETATM 9 H H012 VTY . . . D 3 9.298 11.237 8.411 1 64.68 ? H012 VTY 403 A 1 HETATM 10 H H013 VTY . . . D 3 10.438 10.931 9.728 1 64.68 ? H013 VTY 403 A 1 HETATM 11 H H011 VTY . . . D 3 9.545 12.457 9.667 1 64.68 ? H011 VTY 403 A 1 HETATM 12 H H031 VTY . . . D 3 6.562 11.665 9.539 1 79.84 ? H031 VTY 403 A 1 HETATM 13 H H041 VTY . . . D 3 6.512 11.687 12.313 1 71.2 ? H041 VTY 403 A 1 HETATM 14 H H081 VTY . . . D 3 4.696 10.689 12.154 1 89.95 ? H081 VTY 403 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #