data_8GKR # _model_server_result.job_id jg8QGTOLSw8sFYBVC25rFA _model_server_result.datetime_utc '2024-10-18 19:24:10' _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 8gkr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 8GKR # _exptl.entry_id 8GKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _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 8GKR _cell.length_a 97.907 _cell.length_b 97.907 _cell.length_c 81.008 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKR _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,L,M _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 ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I 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 OD1 ASP 13 A ASP 13 1_555 J CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc2 A OD1 ASP 13 A ASP 13 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc3 A OD2 ASP 13 A ASP 13 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc4 A O MET 14 A MET 14 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A OD1 ASP 115 A ASP 115 1_555 J CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.159 ? metalc ? metalc6 A OD2 ASP 115 A ASP 115 1_555 J CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc7 A OD2 ASP 115 A ASP 115 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc8 A OE2 GLU 116 A GLU 116 1_555 J CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc9 D O10 B7P . A B7P 501 1_555 J CA CA . A CA 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc10 D O10 B7P . A B7P 501 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc11 D O15 B7P . A B7P 501 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc12 D O19 B7P . A B7P 501 1_555 K CA CA . A CA 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc13 J CA CA . A CA 507 1_555 C O3' DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? hydrog WATSON-CRICK hydrog1 B N3 DC 5 T DC 5 1_555 C N1 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 5 T DC 5 1_555 C O6 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 5 T DC 5 1_555 C N2 DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 7 T DC 7 1_555 C N1 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 7 T DC 7 1_555 C O6 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 7 T DC 7 1_555 C N2 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 10 T DA 10 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 10 T DA 10 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 322 n n C1 C2 GOL sing 323 n n C1 H11 GOL sing 324 n n C1 H12 GOL sing 325 n n O1 HO1 GOL sing 326 n n C2 O2 GOL sing 327 n n C2 C3 GOL sing 328 n n C2 H2 GOL sing 329 n n O2 HO2 GOL sing 330 n n C3 O3 GOL sing 331 n n C3 H31 GOL sing 332 n n C3 H32 GOL sing 333 n n O3 HO3 GOL sing 334 n n # _atom_sites.entry_id 8GKR _atom_sites.fract_transf_matrix[1][1] 0.010214 _atom_sites.fract_transf_matrix[1][2] 0.005897 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011794 _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] 0.012344 _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 D 4 B7P A 1 501 501 B7P B7P . E 5 GOL A 1 502 502 GOL GOL . F 5 GOL A 1 503 503 GOL GOL . G 5 GOL A 1 504 504 GOL GOL . H 5 GOL A 1 505 505 GOL GOL . I 5 GOL A 1 506 506 GOL GOL . J 6 CA A 1 507 1 CA CA . K 6 CA A 1 508 2 CA CA . L 7 HOH A 1 601 1 HOH HOH . L 7 HOH A 2 602 2 HOH HOH . L 7 HOH A 3 603 5 HOH HOH . L 7 HOH A 4 604 3 HOH HOH . M 7 HOH P 1 101 4 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 . . . E 5 -45.507 16.52 -0.641 1 51.98 ? C1 GOL 502 A 1 HETATM 2 O O1 GOL . . . E 5 -46.418 15.956 0.212 1 44.28 ? O1 GOL 502 A 1 HETATM 3 C C2 GOL . . . E 5 -46.315 17.556 -1.436 1 55.98 ? C2 GOL 502 A 1 HETATM 4 O O2 GOL . . . E 5 -45.687 18.801 -1.441 1 57.82 ? O2 GOL 502 A 1 HETATM 5 C C3 GOL . . . E 5 -46.566 16.92 -2.89 1 57.6 ? C3 GOL 502 A 1 HETATM 6 O O3 GOL . . . E 5 -47.048 17.949 -3.778 1 48.32 ? O3 GOL 502 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #