data_4DN5 # _model_server_result.job_id Fw55ulVPARE-yieQc4w8cQ _model_server_result.datetime_utc '2024-10-22 00:23:13' _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 4dn5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1002}' # _entry.id 4DN5 # _exptl.entry_id 4DN5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 6 _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 4DN5 _cell.length_a 85.06 _cell.length_b 85.06 _cell.length_c 115.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DN5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,N 1 1 B,K,L,M,O 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 3 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 ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 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 ASN 196 A ASN 520 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc2 A OD2 ASP 210 A ASP 534 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc3 C MG MG . A MG 1001 1_555 J O1A AGS . A AGS 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc4 C MG MG . A MG 1001 1_555 J O2B AGS . A AGS 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc5 C MG MG . A MG 1001 1_555 N O HOH . A HOH 1118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 C MG MG . A MG 1001 1_555 N O HOH . A HOH 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc7 B OD1 ASN 196 B ASN 520 1_555 K MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 B OD1 ASP 210 B ASP 534 1_555 K MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc9 K MG MG . B MG 1001 1_555 M O2A AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc10 K MG MG . B MG 1001 1_555 M O2B AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc11 K MG MG . B MG 1001 1_555 O O HOH . B HOH 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc12 K MG MG . B MG 1001 1_555 O O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? # _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 132 n n C1 C2 EDO sing 133 n n C1 H11 EDO sing 134 n n C1 H12 EDO sing 135 n n O1 HO1 EDO sing 136 n n C2 O2 EDO sing 137 n n C2 H21 EDO sing 138 n n C2 H22 EDO sing 139 n n O2 HO2 EDO sing 140 n n # _atom_sites.entry_id 4DN5 _atom_sites.fract_transf_matrix[1][1] 0.011756 _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] 0.011756 _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] 0.008666 _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 MG A 1 1001 1001 MG MG . D 3 GOL A 1 1002 1 GOL GOL . E 4 EDO A 1 1003 2 EDO EDO . F 4 EDO A 1 1004 3 EDO EDO . G 4 EDO A 1 1005 4 EDO EDO . H 4 EDO A 1 1006 5 EDO EDO . I 4 EDO A 1 1007 7 EDO EDO . J 5 AGS A 1 1008 1 AGS AGS . K 2 MG B 1 1001 1001 MG MG . L 4 EDO B 1 1002 6 EDO EDO . M 5 AGS B 1 1003 1 AGS AGS . N 6 HOH A 1 1101 1 HOH HOH . N 6 HOH A 2 1102 2 HOH HOH . N 6 HOH A 3 1103 7 HOH HOH . N 6 HOH A 4 1104 9 HOH HOH . N 6 HOH A 5 1105 10 HOH HOH . N 6 HOH A 6 1106 11 HOH HOH . N 6 HOH A 7 1107 12 HOH HOH . N 6 HOH A 8 1108 14 HOH HOH . N 6 HOH A 9 1109 15 HOH HOH . N 6 HOH A 10 1110 18 HOH HOH . N 6 HOH A 11 1111 19 HOH HOH . N 6 HOH A 12 1112 20 HOH HOH . N 6 HOH A 13 1113 21 HOH HOH . N 6 HOH A 14 1114 22 HOH HOH . N 6 HOH A 15 1115 23 HOH HOH . N 6 HOH A 16 1116 24 HOH HOH . N 6 HOH A 17 1117 25 HOH HOH . N 6 HOH A 18 1118 28 HOH HOH . N 6 HOH A 19 1119 29 HOH HOH . N 6 HOH A 20 1120 30 HOH HOH . N 6 HOH A 21 1121 31 HOH HOH . N 6 HOH A 22 1122 32 HOH HOH . N 6 HOH A 23 1123 33 HOH HOH . N 6 HOH A 24 1124 34 HOH HOH . N 6 HOH A 25 1125 37 HOH HOH . N 6 HOH A 26 1126 38 HOH HOH . N 6 HOH A 27 1127 39 HOH HOH . N 6 HOH A 28 1128 40 HOH HOH . N 6 HOH A 29 1129 41 HOH HOH . N 6 HOH A 30 1130 42 HOH HOH . N 6 HOH A 31 1131 43 HOH HOH . N 6 HOH A 32 1132 44 HOH HOH . N 6 HOH A 33 1133 45 HOH HOH . N 6 HOH A 34 1134 46 HOH HOH . N 6 HOH A 35 1135 47 HOH HOH . N 6 HOH A 36 1136 48 HOH HOH . N 6 HOH A 37 1137 49 HOH HOH . N 6 HOH A 38 1138 50 HOH HOH . N 6 HOH A 39 1139 51 HOH HOH . N 6 HOH A 40 1140 65 HOH HOH . N 6 HOH A 41 1141 66 HOH HOH . N 6 HOH A 42 1142 67 HOH HOH . N 6 HOH A 43 1143 68 HOH HOH . N 6 HOH A 44 1144 70 HOH HOH . N 6 HOH A 45 1145 71 HOH HOH . N 6 HOH A 46 1146 72 HOH HOH . O 6 HOH B 1 1101 3 HOH HOH . O 6 HOH B 2 1102 4 HOH HOH . O 6 HOH B 3 1103 5 HOH HOH . O 6 HOH B 4 1104 6 HOH HOH . O 6 HOH B 5 1105 8 HOH HOH . O 6 HOH B 6 1106 13 HOH HOH . O 6 HOH B 7 1107 16 HOH HOH . O 6 HOH B 8 1108 26 HOH HOH . O 6 HOH B 9 1109 27 HOH HOH . O 6 HOH B 10 1110 35 HOH HOH . O 6 HOH B 11 1111 52 HOH HOH . O 6 HOH B 12 1112 53 HOH HOH . O 6 HOH B 13 1113 54 HOH HOH . O 6 HOH B 14 1114 55 HOH HOH . O 6 HOH B 15 1115 56 HOH HOH . O 6 HOH B 16 1116 57 HOH HOH . O 6 HOH B 17 1117 58 HOH HOH . O 6 HOH B 18 1118 59 HOH HOH . O 6 HOH B 19 1119 60 HOH HOH . O 6 HOH B 20 1120 61 HOH HOH . O 6 HOH B 21 1121 62 HOH HOH . O 6 HOH B 22 1122 63 HOH HOH . O 6 HOH B 23 1123 64 HOH HOH . O 6 HOH B 24 1124 69 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 . . . L 4 -10.154 48.96 -25.573 1 47.8 ? C1 EDO 1002 B 1 HETATM 2 O O1 EDO . . . L 4 -11.418 49.607 -25.381 1 48.94 ? O1 EDO 1002 B 1 HETATM 3 C C2 EDO . . . L 4 -9.072 50.014 -25.761 1 47.91 ? C2 EDO 1002 B 1 HETATM 4 O O2 EDO . . . L 4 -8.513 50.377 -24.488 1 47.86 ? O2 EDO 1002 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 4 #