data_8GDX # _model_server_result.job_id ZL2dvTaTTP2DK7lwPSQthg _model_server_result.datetime_utc '2024-11-15 17:51:01' _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 8gdx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":406}' # _entry.id 8GDX # _exptl.entry_id 8GDX _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 90 _cell.angle_gamma 90 _cell.entry_id 8GDX _cell.length_a 81.439 _cell.length_b 81.439 _cell.length_c 81.439 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GDX _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _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,H,I _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 G N N ? 3 H 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 metalc ? metalc1 A SG CYS 7 A CYS 206 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 A SG CYS 10 A CYS 209 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc3 A SG CYS 24 A CYS 223 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc4 A SG CYS 27 A CYS 226 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 A ND1 HIS 32 A HIS 231 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc6 A SG CYS 35 A CYS 234 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc7 A SG CYS 48 A CYS 247 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc8 A SG CYS 51 A CYS 250 1_555 F ZN ZN . A ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc9 A SG CYS 59 A CYS 258 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc10 A SG CYS 62 A CYS 261 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc11 A ND1 HIS 80 A HIS 279 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc12 A SG CYS 83 A CYS 282 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc13 A SG CYS 116 A CYS 315 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc14 A SG CYS 119 A CYS 318 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc15 A SG CYS 129 A CYS 328 1_555 E ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc16 A SG CYS 134 A CYS 333 1_555 E ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc17 A ND1 HIS 139 A HIS 338 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc18 A SG CYS 142 A CYS 341 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc19 A SG CYS 166 A CYS 365 1_555 E ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc20 A ND1 HIS 169 A HIS 368 1_555 E ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? # _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 8GDX _atom_sites.fract_transf_matrix[1][1] 0.012279 _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] 0.012279 _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] 0.012279 _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 ZN A 1 401 401 ZN ZN . C 2 ZN A 1 402 402 ZN ZN . D 2 ZN A 1 403 403 ZN ZN . E 2 ZN A 1 404 404 ZN ZN . F 2 ZN A 1 405 405 ZN ZN . G 3 GOL A 1 406 406 GOL GOL . H 3 GOL A 1 407 407 GOL GOL . I 4 HOH A 1 501 501 HOH HOH . I 4 HOH A 2 502 502 HOH HOH . I 4 HOH A 3 503 503 HOH HOH . I 4 HOH A 4 504 504 HOH HOH . I 4 HOH A 5 505 505 HOH HOH . I 4 HOH A 6 506 506 HOH HOH . I 4 HOH A 7 507 507 HOH HOH . I 4 HOH A 8 508 508 HOH HOH . I 4 HOH A 9 509 509 HOH HOH . I 4 HOH A 10 510 510 HOH HOH . I 4 HOH A 11 511 511 HOH HOH . I 4 HOH A 12 512 512 HOH HOH . I 4 HOH A 13 513 513 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 . . . G 3 27.945 -18.916 2.636 1 78.48 ? C1 GOL 406 A 1 HETATM 2 O O1 GOL . . . G 3 26.589 -18.888 3.096 1 88.43 ? O1 GOL 406 A 1 HETATM 3 C C2 GOL . . . G 3 28.079 -20.022 1.632 1 75.98 ? C2 GOL 406 A 1 HETATM 4 O O2 GOL . . . G 3 29.059 -19.777 0.675 1 71.31 ? O2 GOL 406 A 1 HETATM 5 C C3 GOL . . . G 3 28.494 -21.265 2.431 1 72.74 ? C3 GOL 406 A 1 HETATM 6 O O3 GOL . . . G 3 28.013 -22.327 1.697 1 69.36 ? O3 GOL 406 A 1 HETATM 7 H H11 GOL . . . G 3 28.211 -18.08 2.221 1 94.42 ? H11 GOL 406 A 1 HETATM 8 H H12 GOL . . . G 3 28.575 -19.067 3.357 1 94.42 ? H12 GOL 406 A 1 HETATM 9 H HO1 GOL . . . G 3 26.622 -18.827 3.943 1 106.37 ? HO1 GOL 406 A 1 HETATM 10 H H2 GOL . . . G 3 27.227 -20.117 1.179 1 91.42 ? H2 GOL 406 A 1 HETATM 11 H HO2 GOL . . . G 3 29.78 -19.586 1.082 1 85.82 ? HO2 GOL 406 A 1 HETATM 12 H H31 GOL . . . G 3 29.457 -21.272 2.545 1 87.53 ? H31 GOL 406 A 1 HETATM 13 H H32 GOL . . . G 3 28.13 -21.212 3.328 1 87.53 ? H32 GOL 406 A 1 HETATM 14 H HO3 GOL . . . G 3 28.085 -23.017 2.189 1 83.48 ? HO3 GOL 406 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #