data_5JSX # _model_server_result.job_id eJFu3YJ3TO0BudcUd7xnqQ _model_server_result.datetime_utc '2025-01-09 22:08:21' _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 5jsx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5JSX # _exptl.entry_id 5JSX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 5JSX _cell.length_a 98.78 _cell.length_b 98.78 _cell.length_c 127.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JSX _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 A OD2 ASP 140 A ASP 136 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc2 A ND1 HIS 262 A HIS 258 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc3 B MN MN . A MN 401 1_555 C O2B UPG . A UPG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 B MN MN . A MN 401 1_555 C O1A UPG . A UPG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc5 B MN MN . A MN 401 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc6 B MN MN . A MN 401 1_555 E O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 5JSX _atom_sites.fract_transf_matrix[1][1] 0.010124 _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] 0.010124 _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] 0.007817 _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 MN A 1 401 1 MN MN . C 3 UPG A 1 402 2 UPG UPG . D 4 GOL A 1 403 1 GOL GOL . E 5 HOH A 1 501 3 HOH HOH . E 5 HOH A 2 502 25 HOH HOH . E 5 HOH A 3 503 61 HOH HOH . E 5 HOH A 4 504 71 HOH HOH . E 5 HOH A 5 505 34 HOH HOH . E 5 HOH A 6 506 18 HOH HOH . E 5 HOH A 7 507 24 HOH HOH . E 5 HOH A 8 508 5 HOH HOH . E 5 HOH A 9 509 2 HOH HOH . E 5 HOH A 10 510 70 HOH HOH . E 5 HOH A 11 511 54 HOH HOH . E 5 HOH A 12 512 9 HOH HOH . E 5 HOH A 13 513 11 HOH HOH . E 5 HOH A 14 514 72 HOH HOH . E 5 HOH A 15 515 62 HOH HOH . E 5 HOH A 16 516 41 HOH HOH . E 5 HOH A 17 517 69 HOH HOH . E 5 HOH A 18 518 40 HOH HOH . E 5 HOH A 19 519 37 HOH HOH . E 5 HOH A 20 520 27 HOH HOH . E 5 HOH A 21 521 63 HOH HOH . E 5 HOH A 22 522 19 HOH HOH . E 5 HOH A 23 523 67 HOH HOH . E 5 HOH A 24 524 44 HOH HOH . E 5 HOH A 25 525 22 HOH HOH . E 5 HOH A 26 526 10 HOH HOH . E 5 HOH A 27 527 59 HOH HOH . E 5 HOH A 28 528 7 HOH HOH . E 5 HOH A 29 529 51 HOH HOH . E 5 HOH A 30 530 45 HOH HOH . E 5 HOH A 31 531 68 HOH HOH . E 5 HOH A 32 532 35 HOH HOH . E 5 HOH A 33 533 12 HOH HOH . E 5 HOH A 34 534 42 HOH HOH . E 5 HOH A 35 535 21 HOH HOH . E 5 HOH A 36 536 20 HOH HOH . E 5 HOH A 37 537 48 HOH HOH . E 5 HOH A 38 538 60 HOH HOH . E 5 HOH A 39 539 65 HOH HOH . E 5 HOH A 40 540 55 HOH HOH . E 5 HOH A 41 541 23 HOH HOH . E 5 HOH A 42 542 66 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 4 8.465 -1.61 -29.26 1 83.88 ? C1 GOL 403 A 1 HETATM 2 O O1 GOL . . . D 4 7.222 -1.101 -29.641 1 83.88 ? O1 GOL 403 A 1 HETATM 3 C C2 GOL . . . D 4 9.235 -1.587 -30.55 1 83.88 ? C2 GOL 403 A 1 HETATM 4 O O2 GOL . . . D 4 9.06 -2.903 -31.055 1 83.88 ? O2 GOL 403 A 1 HETATM 5 C C3 GOL . . . D 4 10.687 -1.056 -30.435 1 83.88 ? C3 GOL 403 A 1 HETATM 6 O O3 GOL . . . D 4 11.131 -0.425 -31.644 1 83.88 ? O3 GOL 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #