data_8VZK # _model_server_result.job_id q5rR8N74vITiJC2zFD1mXA _model_server_result.datetime_utc '2024-11-18 07:54:23' _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 8vzk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":605}' # _entry.id 8VZK # _exptl.entry_id 8VZK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _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 8VZK _cell.length_a 111.327 _cell.length_b 111.327 _cell.length_c 193.164 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VZK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 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,L,M,N _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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -64.388 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 L 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 446 A ASP 448 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc2 A OD1 ASN 473 A ASN 475 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc3 A O GLY 475 A GLY 477 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc4 C O2A TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc5 C O1B TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 C O2B TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc7 B OD1 ASP 446 B ASP 448 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 B OD1 ASN 473 B ASN 475 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc9 I O2A TPP . B TPP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc10 I O1B TPP . B TPP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 EDO sing 127 n n C1 C2 EDO sing 128 n n C1 H11 EDO sing 129 n n C1 H12 EDO sing 130 n n O1 HO1 EDO sing 131 n n C2 O2 EDO sing 132 n n C2 H21 EDO sing 133 n n C2 H22 EDO sing 134 n n O2 HO2 EDO sing 135 n n # _atom_sites.entry_id 8VZK _atom_sites.fract_transf_matrix[1][1] 0.008983 _atom_sites.fract_transf_matrix[1][2] 0.005186 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010372 _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] 0.005177 _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 C 2 TPP A 1 601 601 TPP TPP . D 3 ADP A 1 602 602 ADP ADP . E 4 MG A 1 603 605 MG MG . F 5 EDO A 1 604 611 EDO EDO . G 5 EDO A 1 605 612 EDO EDO . H 6 PEG A 1 606 613 PEG PEG . I 2 TPP B 1 601 601 TPP TPP . J 3 ADP B 1 602 602 ADP ADP . K 4 MG B 1 603 605 MG MG . L 5 EDO B 1 604 611 EDO EDO . M 7 HOH A 1 701 4 HOH HOH . N 7 HOH B 1 701 3 HOH HOH . N 7 HOH B 2 702 2 HOH HOH . N 7 HOH B 3 703 1 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 EDO . . . G 5 68.149 -43.192 -3.944 1 89.36 ? C1 EDO 605 A 1 HETATM 2 O O1 EDO . . . G 5 66.759 -43.491 -4.116 1 88.1 ? O1 EDO 605 A 1 HETATM 3 C C2 EDO . . . G 5 68.398 -42.753 -2.506 1 87.66 ? C2 EDO 605 A 1 HETATM 4 O O2 EDO . . . G 5 67.586 -41.611 -2.213 1 84.71 ? O2 EDO 605 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 4 #