data_8RPD # _model_server_result.job_id xTlut-zhCDhxqE8F1AkU0A _model_server_result.datetime_utc '2025-07-15 15:20:18' _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 8rpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 8RPD # _exptl.entry_id 8RPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _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 120 _cell.entry_id 8RPD _cell.length_a 56.816 _cell.length_b 56.816 _cell.length_c 59.78 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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,x-y,-z 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 23 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 23 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 94 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 94 _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 2.059 _struct_conn.pdbx_value_order ? # _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 8RPD _atom_sites.fract_transf_matrix[1][1] 0.017601 _atom_sites.fract_transf_matrix[1][2] 0.010162 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020324 _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] 0.016728 _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 1 201 205 GOL GOL . C 2 GOL A 1 202 206 GOL GOL . D 2 GOL A 1 203 207 GOL GOL . E 3 HOH A 1 301 75 HOH HOH . E 3 HOH A 2 302 63 HOH HOH . E 3 HOH A 3 303 28 HOH HOH . E 3 HOH A 4 304 34 HOH HOH . E 3 HOH A 5 305 59 HOH HOH . E 3 HOH A 6 306 81 HOH HOH . E 3 HOH A 7 307 31 HOH HOH . E 3 HOH A 8 308 66 HOH HOH . E 3 HOH A 9 309 19 HOH HOH . E 3 HOH A 10 310 12 HOH HOH . E 3 HOH A 11 311 24 HOH HOH . E 3 HOH A 12 312 71 HOH HOH . E 3 HOH A 13 313 57 HOH HOH . E 3 HOH A 14 314 67 HOH HOH . E 3 HOH A 15 315 4 HOH HOH . E 3 HOH A 16 316 53 HOH HOH . E 3 HOH A 17 317 32 HOH HOH . E 3 HOH A 18 318 61 HOH HOH . E 3 HOH A 19 319 52 HOH HOH . E 3 HOH A 20 320 74 HOH HOH . E 3 HOH A 21 321 82 HOH HOH . E 3 HOH A 22 322 51 HOH HOH . E 3 HOH A 23 323 27 HOH HOH . E 3 HOH A 24 324 17 HOH HOH . E 3 HOH A 25 325 83 HOH HOH . E 3 HOH A 26 326 47 HOH HOH . E 3 HOH A 27 327 2 HOH HOH . E 3 HOH A 28 328 50 HOH HOH . E 3 HOH A 29 329 26 HOH HOH . E 3 HOH A 30 330 73 HOH HOH . E 3 HOH A 31 331 10 HOH HOH . E 3 HOH A 32 332 46 HOH HOH . E 3 HOH A 33 333 55 HOH HOH . E 3 HOH A 34 334 48 HOH HOH . E 3 HOH A 35 335 29 HOH HOH . E 3 HOH A 36 336 60 HOH HOH . E 3 HOH A 37 337 45 HOH HOH . E 3 HOH A 38 338 79 HOH HOH . E 3 HOH A 39 339 18 HOH HOH . E 3 HOH A 40 340 35 HOH HOH . E 3 HOH A 41 341 14 HOH HOH . E 3 HOH A 42 342 41 HOH HOH . E 3 HOH A 43 343 20 HOH HOH . E 3 HOH A 44 344 44 HOH HOH . E 3 HOH A 45 345 49 HOH HOH . E 3 HOH A 46 346 76 HOH HOH . E 3 HOH A 47 347 13 HOH HOH . E 3 HOH A 48 348 21 HOH HOH . E 3 HOH A 49 349 23 HOH HOH . E 3 HOH A 50 350 43 HOH HOH . E 3 HOH A 51 351 54 HOH HOH . E 3 HOH A 52 352 6 HOH HOH . E 3 HOH A 53 353 9 HOH HOH . E 3 HOH A 54 354 25 HOH HOH . E 3 HOH A 55 355 3 HOH HOH . E 3 HOH A 56 356 80 HOH HOH . E 3 HOH A 57 357 5 HOH HOH . E 3 HOH A 58 358 68 HOH HOH . E 3 HOH A 59 359 7 HOH HOH . E 3 HOH A 60 360 72 HOH HOH . E 3 HOH A 61 361 78 HOH HOH . E 3 HOH A 62 362 42 HOH HOH . E 3 HOH A 63 363 65 HOH HOH . E 3 HOH A 64 364 64 HOH HOH . E 3 HOH A 65 365 70 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 . A . C 2 -28.562 4.843 12.47 0.5 23.99 0 C1 GOL 202 A 1 HETATM 2 O O1 GOL . A . C 2 -27.663 4.83 13.574 0.5 26.28 0 O1 GOL 202 A 1 HETATM 3 C C2 GOL . A . C 2 -28.058 3.985 11.329 0.5 23.17 0 C2 GOL 202 A 1 HETATM 4 O O2 GOL . A . C 2 -29.099 3.166 10.802 0.5 25.56 0 O2 GOL 202 A 1 HETATM 5 C C3 GOL . A . C 2 -27.559 4.786 10.161 0.5 21.69 0 C3 GOL 202 A 1 HETATM 6 O O3 GOL . A . C 2 -28.446 4.552 9.078 0.5 20.78 0 O3 GOL 202 A 1 HETATM 7 H H11 GOL . . . C 2 -28.665 5.771 12.151 0.5 24.35 0 H11 GOL 202 A 1 HETATM 8 H H12 GOL . . . C 2 -29.445 4.514 12.758 0.5 24.34 0 H12 GOL 202 A 1 HETATM 9 H HO1 GOL . . . C 2 -28.032 5.467 14.139 0 20 0 HO1 GOL 202 A 1 HETATM 10 H H2 GOL . . . C 2 -27.327 3.41 11.659 0.5 23.48 0 H2 GOL 202 A 1 HETATM 11 H HO2 GOL . . . C 2 -29.128 3.369 9.942 0 20 0 HO2 GOL 202 A 1 HETATM 12 H H31 GOL . . . C 2 -26.645 4.498 9.92 0.5 21.79 0 H31 GOL 202 A 1 HETATM 13 H H32 GOL . . . C 2 -27.547 5.747 10.39 0.5 21.79 0 H32 GOL 202 A 1 HETATM 14 H HO3 GOL . . . C 2 -29.046 4.015 9.337 0.5 21.05 0 HO3 GOL 202 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 627 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #