data_5YVA # _model_server_result.job_id Qp2mm_S3PBtMrBPSjYYuPA _model_server_result.datetime_utc '2024-12-01 07:32:42' _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 5yva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 5YVA # _exptl.entry_id 5YVA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 5YVA _cell.length_a 67.091 _cell.length_b 77.117 _cell.length_c 84.423 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVA _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 ? _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,F,G _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N 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 covale ? covale1 A C MET 246 A MET 396 1_555 A N CAS 247 A CAS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C CAS 247 A CAS 397 1_555 A N LEU 248 A LEU 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 183 n n C1 C2 GOL sing 184 n n C1 H11 GOL sing 185 n n C1 H12 GOL sing 186 n n O1 HO1 GOL sing 187 n n C2 O2 GOL sing 188 n n C2 C3 GOL sing 189 n n C2 H2 GOL sing 190 n n O2 HO2 GOL sing 191 n n C3 O3 GOL sing 192 n n C3 H31 GOL sing 193 n n C3 H32 GOL sing 194 n n O3 HO3 GOL sing 195 n n # _atom_sites.entry_id 5YVA _atom_sites.fract_transf_matrix[1][1] 0.014905 _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] 0.012967 _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] 0.011845 _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 91X A 1 501 501 91X C10 . C 3 GOL A 1 502 601 GOL GOL . D 3 GOL A 1 503 602 GOL GOL . E 3 GOL A 1 504 603 GOL GOL . F 4 CL A 1 505 701 CL CL . G 5 HOH A 1 601 24 HOH HOH . G 5 HOH A 2 602 7 HOH HOH . G 5 HOH A 3 603 21 HOH HOH . G 5 HOH A 4 604 27 HOH HOH . G 5 HOH A 5 605 15 HOH HOH . G 5 HOH A 6 606 1 HOH HOH . G 5 HOH A 7 607 3 HOH HOH . G 5 HOH A 8 608 2 HOH HOH . G 5 HOH A 9 609 14 HOH HOH . G 5 HOH A 10 610 22 HOH HOH . G 5 HOH A 11 611 17 HOH HOH . G 5 HOH A 12 612 8 HOH HOH . G 5 HOH A 13 613 29 HOH HOH . G 5 HOH A 14 614 28 HOH HOH . G 5 HOH A 15 615 9 HOH HOH . G 5 HOH A 16 616 10 HOH HOH . G 5 HOH A 17 617 26 HOH HOH . G 5 HOH A 18 618 35 HOH HOH . G 5 HOH A 19 619 18 HOH HOH . G 5 HOH A 20 620 36 HOH HOH . G 5 HOH A 21 621 19 HOH HOH . G 5 HOH A 22 622 33 HOH HOH . G 5 HOH A 23 623 6 HOH HOH . G 5 HOH A 24 624 32 HOH HOH . G 5 HOH A 25 625 16 HOH HOH . G 5 HOH A 26 626 13 HOH HOH . G 5 HOH A 27 627 37 HOH HOH . G 5 HOH A 28 628 25 HOH HOH . G 5 HOH A 29 629 41 HOH HOH . G 5 HOH A 30 630 42 HOH HOH . G 5 HOH A 31 631 11 HOH HOH . G 5 HOH A 32 632 40 HOH HOH . G 5 HOH A 33 633 30 HOH HOH . G 5 HOH A 34 634 4 HOH HOH . G 5 HOH A 35 635 31 HOH HOH . G 5 HOH A 36 636 20 HOH HOH . G 5 HOH A 37 637 12 HOH HOH . G 5 HOH A 38 638 39 HOH HOH . G 5 HOH A 39 639 5 HOH HOH . G 5 HOH A 40 640 38 HOH HOH . G 5 HOH A 41 641 23 HOH HOH . G 5 HOH A 42 642 34 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 C1 GOL . . . D 3 1.451 -36.077 18.756 1 76.42 ? C1 GOL 503 A 1 HETATM 2 O O1 GOL . . . D 3 2.337 -35.642 17.752 1 73.06 ? O1 GOL 503 A 1 HETATM 3 C C2 GOL . . . D 3 0.913 -34.818 19.634 1 78.04 ? C2 GOL 503 A 1 HETATM 4 O O2 GOL . . . D 3 1.885 -34.205 20.467 1 68.94 ? O2 GOL 503 A 1 HETATM 5 C C3 GOL . . . D 3 0.195 -33.833 18.649 1 72.2 ? C3 GOL 503 A 1 HETATM 6 O O3 GOL . . . D 3 -0.785 -33.117 19.377 1 67.67 ? O3 GOL 503 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #