data_5CDY # _model_server_result.job_id EdKGk7TlLnm4zDhgiwbvdw _model_server_result.datetime_utc '2024-11-05 01:28:42' _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 5cdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":500}' # _entry.id 5CDY # _exptl.entry_id 5CDY _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.91 _cell.angle_gamma 90 _cell.entry_id 5CDY _cell.length_a 64.74 _cell.length_b 96.85 _cell.length_c 71.55 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,F,G,H,I,J,K _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 F N N ? 3 G N N # _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 5CDY _atom_sites.fract_transf_matrix[1][1] 0.015446 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004113 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010325 _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] 0.014463 _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 E 2 PO4 A 1 301 1 PO4 PO4 . F 3 GOL B 1 500 500 GOL GOL . G 3 GOL C 1 500 500 GOL GOL . H 4 HOH A 1 401 8 HOH HOH . H 4 HOH A 2 402 2 HOH HOH . H 4 HOH A 3 403 13 HOH HOH . H 4 HOH A 4 404 11 HOH HOH . H 4 HOH A 5 405 12 HOH HOH . H 4 HOH A 6 406 7 HOH HOH . I 4 HOH B 1 601 10 HOH HOH . I 4 HOH B 2 602 4 HOH HOH . I 4 HOH B 3 603 9 HOH HOH . J 4 HOH C 1 601 5 HOH HOH . J 4 HOH C 2 602 15 HOH HOH . J 4 HOH C 3 603 1 HOH HOH . K 4 HOH D 1 301 14 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 . . . F 3 38.025 2.099 14.096 1 71.73 ? C1 GOL 500 B 1 HETATM 2 O O1 GOL . . . F 3 38.753 1.579 13.006 1 85.01 ? O1 GOL 500 B 1 HETATM 3 C C2 GOL . . . F 3 38.34 1.318 15.355 1 62.56 ? C2 GOL 500 B 1 HETATM 4 O O2 GOL . . . F 3 39.459 1.866 16.024 1 67.78 ? O2 GOL 500 B 1 HETATM 5 C C3 GOL . . . F 3 37.174 1.299 16.31 1 50.45 ? C3 GOL 500 B 1 HETATM 6 O O3 GOL . . . F 3 37.562 0.616 17.448 1 40.44 ? O3 GOL 500 B 1 HETATM 7 H H11 GOL . . . F 3 38.313 3.138 14.235 1 86.08 ? H11 GOL 500 B 1 HETATM 8 H H12 GOL . . . F 3 36.959 2.06 13.886 1 86.08 ? H12 GOL 500 B 1 HETATM 9 H HO1 GOL . . . F 3 38.966 2.3 12.403 1 102.02 ? HO1 GOL 500 B 1 HETATM 10 H H2 GOL . . . F 3 38.563 0.287 15.059 1 75.07 ? H2 GOL 500 B 1 HETATM 11 H HO2 GOL . . . F 3 39.453 2.826 15.929 1 81.34 ? HO2 GOL 500 B 1 HETATM 12 H H31 GOL . . . F 3 36.885 2.306 16.575 1 60.55 ? H31 GOL 500 B 1 HETATM 13 H H32 GOL . . . F 3 36.32 0.799 15.871 1 60.55 ? H32 GOL 500 B 1 HETATM 14 H HO3 GOL . . . F 3 36.908 -0.066 17.624 1 48.53 ? HO3 GOL 500 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #