data_1GFZ # _model_server_result.job_id OgesqqJ3G7hpiA77jnPk1A _model_server_result.datetime_utc '2024-11-25 11:10:00' _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 1gfz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":999}' # _entry.id 1GFZ # _exptl.entry_id 1GFZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 1GFZ _cell.length_a 128.296 _cell.length_b 128.296 _cell.length_c 116.377 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GFZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 116.377 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 680 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 680 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 999 _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 1.339 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 323 n y N1 C6 PLP sing 324 n y C2 C2A PLP sing 325 n n C2 C3 PLP sing 326 n y C2A H2A1 PLP sing 327 n n C2A H2A2 PLP sing 328 n n C2A H2A3 PLP sing 329 n n C3 O3 PLP sing 330 n n C3 C4 PLP doub 331 n y O3 HO3 PLP sing 332 n n C4 C4A PLP sing 333 n n C4 C5 PLP sing 334 n y C4A O4A PLP doub 335 n n C4A H4A PLP sing 336 n n C5 C6 PLP doub 337 n y C5 C5A PLP sing 338 n n C6 H6 PLP sing 339 n n C5A O4P PLP sing 340 n n C5A H5A1 PLP sing 341 n n C5A H5A2 PLP sing 342 n n O4P P PLP sing 343 n n P O1P PLP doub 344 n n P O2P PLP sing 345 n n P O3P PLP sing 346 n n O2P HOP2 PLP sing 347 n n O3P HOP3 PLP sing 348 n n # _atom_sites.entry_id 1GFZ _atom_sites.fract_transf_matrix[1][1] 0.007794 _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] 0.007794 _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] 0.008593 _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 PLP A 1 999 999 PLP PLP . C 3 IMP A 1 930 930 IMP IMP . D 4 CFF A 1 940 940 CFF CFF . E 5 HOH A 1 1000 1 HOH HOH . E 5 HOH A 2 1001 2 HOH HOH . E 5 HOH A 3 1002 3 HOH HOH . E 5 HOH A 4 1003 4 HOH HOH . E 5 HOH A 5 1004 5 HOH HOH . E 5 HOH A 6 1005 6 HOH HOH . E 5 HOH A 7 1006 7 HOH HOH . E 5 HOH A 8 1007 8 HOH HOH . E 5 HOH A 9 1008 9 HOH HOH . E 5 HOH A 10 1009 10 HOH HOH . E 5 HOH A 11 1010 11 HOH HOH . E 5 HOH A 12 1011 12 HOH HOH . E 5 HOH A 13 1012 13 HOH HOH . E 5 HOH A 14 1013 14 HOH HOH . E 5 HOH A 15 1014 15 HOH HOH . E 5 HOH A 16 1015 16 HOH HOH . E 5 HOH A 17 1016 17 HOH HOH . E 5 HOH A 18 1017 18 HOH HOH . E 5 HOH A 19 1018 19 HOH HOH . E 5 HOH A 20 1019 20 HOH HOH . E 5 HOH A 21 1020 21 HOH HOH . E 5 HOH A 22 1021 22 HOH HOH . E 5 HOH A 23 1022 23 HOH HOH . E 5 HOH A 24 1023 24 HOH HOH . E 5 HOH A 25 1024 25 HOH HOH . E 5 HOH A 26 1025 26 HOH HOH . E 5 HOH A 27 1026 27 HOH HOH . E 5 HOH A 28 1027 28 HOH HOH . E 5 HOH A 29 1028 29 HOH HOH . E 5 HOH A 30 1029 30 HOH HOH . E 5 HOH A 31 1030 31 HOH HOH . E 5 HOH A 32 1031 32 HOH HOH . E 5 HOH A 33 1032 33 HOH HOH . E 5 HOH A 34 1033 34 HOH HOH . E 5 HOH A 35 1034 35 HOH HOH . E 5 HOH A 36 1035 36 HOH HOH . E 5 HOH A 37 1036 37 HOH HOH . E 5 HOH A 38 1037 38 HOH HOH . E 5 HOH A 39 1038 39 HOH HOH . E 5 HOH A 40 1039 40 HOH HOH . E 5 HOH A 41 1040 41 HOH HOH . E 5 HOH A 42 1041 42 HOH HOH . E 5 HOH A 43 1042 43 HOH HOH . E 5 HOH A 44 1043 44 HOH HOH . E 5 HOH A 45 1044 45 HOH HOH . E 5 HOH A 46 1045 46 HOH HOH . E 5 HOH A 47 1046 47 HOH HOH . E 5 HOH A 48 1047 48 HOH HOH . E 5 HOH A 49 1048 49 HOH HOH . E 5 HOH A 50 1049 50 HOH HOH . E 5 HOH A 51 1050 51 HOH HOH . E 5 HOH A 52 1051 52 HOH HOH . E 5 HOH A 53 1052 53 HOH HOH . E 5 HOH A 54 1053 54 HOH HOH . E 5 HOH A 55 1054 55 HOH HOH . E 5 HOH A 56 1055 56 HOH HOH . E 5 HOH A 57 1056 57 HOH HOH . E 5 HOH A 58 1057 58 HOH HOH . E 5 HOH A 59 1058 59 HOH HOH . E 5 HOH A 60 1059 60 HOH HOH . E 5 HOH A 61 1060 61 HOH HOH . E 5 HOH A 62 1061 62 HOH HOH . E 5 HOH A 63 1062 63 HOH HOH . E 5 HOH A 64 1063 64 HOH HOH . E 5 HOH A 65 1064 65 HOH HOH . E 5 HOH A 66 1065 66 HOH HOH . E 5 HOH A 67 1066 67 HOH HOH . E 5 HOH A 68 1067 68 HOH HOH . E 5 HOH A 69 1068 69 HOH HOH . E 5 HOH A 70 1069 70 HOH HOH . E 5 HOH A 71 1070 71 HOH HOH . E 5 HOH A 72 1071 72 HOH HOH . E 5 HOH A 73 1072 73 HOH HOH . E 5 HOH A 74 1073 74 HOH HOH . E 5 HOH A 75 1074 75 HOH HOH . E 5 HOH A 76 1075 76 HOH HOH . E 5 HOH A 77 1076 77 HOH HOH . E 5 HOH A 78 1077 78 HOH HOH . E 5 HOH A 79 1078 79 HOH HOH . E 5 HOH A 80 1079 80 HOH HOH . E 5 HOH A 81 1080 81 HOH HOH . E 5 HOH A 82 1081 82 HOH HOH . E 5 HOH A 83 1082 83 HOH HOH . E 5 HOH A 84 1083 84 HOH HOH . E 5 HOH A 85 1084 85 HOH HOH . E 5 HOH A 86 1085 86 HOH HOH . E 5 HOH A 87 1086 87 HOH HOH . E 5 HOH A 88 1087 88 HOH HOH . E 5 HOH A 89 1088 89 HOH HOH . E 5 HOH A 90 1089 90 HOH HOH . E 5 HOH A 91 1090 91 HOH HOH . E 5 HOH A 92 1091 92 HOH HOH . E 5 HOH A 93 1092 93 HOH HOH . E 5 HOH A 94 1093 94 HOH HOH . E 5 HOH A 95 1094 95 HOH HOH . E 5 HOH A 96 1095 96 HOH HOH . E 5 HOH A 97 1096 97 HOH HOH . E 5 HOH A 98 1097 98 HOH HOH . E 5 HOH A 99 1098 99 HOH HOH . E 5 HOH A 100 1099 100 HOH HOH . E 5 HOH A 101 1100 101 HOH HOH . E 5 HOH A 102 1101 102 HOH HOH . E 5 HOH A 103 1102 103 HOH HOH . E 5 HOH A 104 1103 104 HOH HOH . E 5 HOH A 105 1104 105 HOH HOH . E 5 HOH A 106 1105 106 HOH HOH . E 5 HOH A 107 1106 107 HOH HOH . E 5 HOH A 108 1107 108 HOH HOH . E 5 HOH A 109 1108 109 HOH HOH . E 5 HOH A 110 1109 110 HOH HOH . E 5 HOH A 111 1110 111 HOH HOH . E 5 HOH A 112 1111 112 HOH HOH . E 5 HOH A 113 1112 113 HOH HOH . E 5 HOH A 114 1113 114 HOH HOH . E 5 HOH A 115 1114 115 HOH HOH . E 5 HOH A 116 1115 116 HOH HOH . E 5 HOH A 117 1116 117 HOH HOH . E 5 HOH A 118 1117 118 HOH HOH . E 5 HOH A 119 1118 119 HOH HOH . E 5 HOH A 120 1119 120 HOH HOH . E 5 HOH A 121 1120 121 HOH HOH . E 5 HOH A 122 1121 122 HOH HOH . E 5 HOH A 123 1122 123 HOH HOH . E 5 HOH A 124 1123 124 HOH HOH . E 5 HOH A 125 1124 125 HOH HOH . E 5 HOH A 126 1125 126 HOH HOH . E 5 HOH A 127 1126 127 HOH HOH . E 5 HOH A 128 1127 128 HOH HOH . E 5 HOH A 129 1128 129 HOH HOH . E 5 HOH A 130 1129 130 HOH HOH . E 5 HOH A 131 1130 131 HOH HOH . E 5 HOH A 132 1131 132 HOH HOH . E 5 HOH A 133 1132 133 HOH HOH . E 5 HOH A 134 1133 134 HOH HOH . E 5 HOH A 135 1134 135 HOH HOH . E 5 HOH A 136 1135 136 HOH HOH . E 5 HOH A 137 1136 137 HOH HOH . E 5 HOH A 138 1137 138 HOH HOH . E 5 HOH A 139 1138 139 HOH HOH . E 5 HOH A 140 1139 140 HOH HOH . E 5 HOH A 141 1140 141 HOH HOH . E 5 HOH A 142 1141 142 HOH HOH . E 5 HOH A 143 1142 143 HOH HOH . E 5 HOH A 144 1143 144 HOH HOH . E 5 HOH A 145 1144 145 HOH HOH . E 5 HOH A 146 1145 146 HOH HOH . E 5 HOH A 147 1146 147 HOH HOH . E 5 HOH A 148 1147 148 HOH HOH . E 5 HOH A 149 1148 149 HOH HOH . E 5 HOH A 150 1149 150 HOH HOH . E 5 HOH A 151 1150 151 HOH HOH . E 5 HOH A 152 1151 152 HOH HOH . E 5 HOH A 153 1152 153 HOH HOH . E 5 HOH A 154 1153 154 HOH HOH . E 5 HOH A 155 1154 155 HOH HOH . E 5 HOH A 156 1155 156 HOH HOH . E 5 HOH A 157 1156 157 HOH HOH . E 5 HOH A 158 1157 158 HOH HOH . E 5 HOH A 159 1158 159 HOH HOH . E 5 HOH A 160 1159 160 HOH HOH . E 5 HOH A 161 1160 161 HOH HOH . E 5 HOH A 162 1161 162 HOH HOH . E 5 HOH A 163 1162 163 HOH HOH . E 5 HOH A 164 1163 164 HOH HOH . E 5 HOH A 165 1164 165 HOH HOH . E 5 HOH A 166 1165 166 HOH HOH . E 5 HOH A 167 1166 167 HOH HOH . E 5 HOH A 168 1167 168 HOH HOH . E 5 HOH A 169 1168 169 HOH HOH . E 5 HOH A 170 1169 170 HOH HOH . E 5 HOH A 171 1170 171 HOH HOH . E 5 HOH A 172 1171 172 HOH HOH . E 5 HOH A 173 1172 173 HOH HOH . E 5 HOH A 174 1173 174 HOH HOH . E 5 HOH A 175 1174 175 HOH HOH . E 5 HOH A 176 1175 176 HOH HOH . E 5 HOH A 177 1176 177 HOH HOH . E 5 HOH A 178 1177 178 HOH HOH . E 5 HOH A 179 1178 179 HOH HOH . E 5 HOH A 180 1179 180 HOH HOH . E 5 HOH A 181 1180 181 HOH HOH . E 5 HOH A 182 1181 182 HOH HOH . E 5 HOH A 183 1182 183 HOH HOH . E 5 HOH A 184 1183 184 HOH HOH . E 5 HOH A 185 1184 185 HOH HOH . E 5 HOH A 186 1185 186 HOH HOH . E 5 HOH A 187 1186 187 HOH HOH . E 5 HOH A 188 1187 188 HOH HOH . E 5 HOH A 189 1188 189 HOH HOH . E 5 HOH A 190 1189 190 HOH HOH . E 5 HOH A 191 1190 191 HOH HOH . E 5 HOH A 192 1191 192 HOH HOH . E 5 HOH A 193 1192 193 HOH HOH . E 5 HOH A 194 1193 194 HOH HOH . E 5 HOH A 195 1194 195 HOH HOH . E 5 HOH A 196 1195 197 HOH HOH . E 5 HOH A 197 1196 198 HOH HOH . E 5 HOH A 198 1197 199 HOH HOH . E 5 HOH A 199 1198 200 HOH HOH . E 5 HOH A 200 1199 201 HOH HOH . E 5 HOH A 201 1200 202 HOH HOH . E 5 HOH A 202 1201 203 HOH HOH . E 5 HOH A 203 1202 204 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 N N1 PLP . . . B 2 24.756 25.64 30.36 1 17.34 ? N1 PLP 999 A 1 HETATM 2 C C2 PLP . . . B 2 23.637 24.894 30.597 1 14.8 ? C2 PLP 999 A 1 HETATM 3 C C2A PLP . . . B 2 22.62 25.456 31.573 1 13.7 ? C2A PLP 999 A 1 HETATM 4 C C3 PLP . . . B 2 23.397 23.752 29.866 1 17.64 ? C3 PLP 999 A 1 HETATM 5 O O3 PLP . . . B 2 22.202 23.131 29.98 1 22.96 ? O3 PLP 999 A 1 HETATM 6 C C4 PLP . . . B 2 24.301 23.362 28.89 1 17.73 ? C4 PLP 999 A 1 HETATM 7 C C4A PLP . . . B 2 24.059 22.092 28.054 1 18.11 ? C4A PLP 999 A 1 HETATM 8 C C5 PLP . . . B 2 25.448 24.149 28.672 1 19.05 ? C5 PLP 999 A 1 HETATM 9 C C6 PLP . . . B 2 25.65 25.276 29.413 1 18.37 ? C6 PLP 999 A 1 HETATM 10 C C5A PLP . . . B 2 26.457 23.872 27.487 1 19.06 ? C5A PLP 999 A 1 HETATM 11 O O4P PLP . . . B 2 26.05 24.566 26.278 1 22.64 ? O4P PLP 999 A 1 HETATM 12 P P PLP . . . B 2 27.012 24.813 25.02 1 18.76 ? P PLP 999 A 1 HETATM 13 O O1P PLP . . . B 2 26.175 25.466 24.001 1 23.9 ? O1P PLP 999 A 1 HETATM 14 O O2P PLP . . . B 2 28.074 25.932 25.519 1 19.72 ? O2P PLP 999 A 1 HETATM 15 O O3P PLP . . . B 2 27.735 23.546 24.725 1 21.2 ? O3P PLP 999 A 1 # _model_server_stats.io_time_ms 115 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #