data_5O56 # _model_server_result.job_id 1CaLRXeInFMhBt0M8dWjTA _model_server_result.datetime_utc '2024-10-13 07:18:58' _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 5o56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 5O56 # _exptl.entry_id 5O56 _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 5O56 _cell.length_a 128.548 _cell.length_b 128.548 _cell.length_c 116.141 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O56 _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 _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 _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 0 116.141 # _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 681 _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 901 _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 1.444 _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' # _atom_sites.entry_id 5O56 _atom_sites.fract_transf_matrix[1][1] 0.007779 _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] 0.007779 _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] 0.00861 _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 1 901 903 PLP PLP . C 3 9L8 A 1 902 1 9L8 29b . D 4 HOH A 1 1001 300 HOH HOH . D 4 HOH A 2 1002 301 HOH HOH . D 4 HOH A 3 1003 260 HOH HOH . D 4 HOH A 4 1004 69 HOH HOH . D 4 HOH A 5 1005 68 HOH HOH . D 4 HOH A 6 1006 108 HOH HOH . D 4 HOH A 7 1007 158 HOH HOH . D 4 HOH A 8 1008 37 HOH HOH . D 4 HOH A 9 1009 101 HOH HOH . D 4 HOH A 10 1010 75 HOH HOH . D 4 HOH A 11 1011 286 HOH HOH . D 4 HOH A 12 1012 211 HOH HOH . D 4 HOH A 13 1013 269 HOH HOH . D 4 HOH A 14 1014 125 HOH HOH . D 4 HOH A 15 1015 298 HOH HOH . D 4 HOH A 16 1016 58 HOH HOH . D 4 HOH A 17 1017 292 HOH HOH . D 4 HOH A 18 1018 15 HOH HOH . D 4 HOH A 19 1019 134 HOH HOH . D 4 HOH A 20 1020 130 HOH HOH . D 4 HOH A 21 1021 36 HOH HOH . D 4 HOH A 22 1022 84 HOH HOH . D 4 HOH A 23 1023 73 HOH HOH . D 4 HOH A 24 1024 305 HOH HOH . D 4 HOH A 25 1025 18 HOH HOH . D 4 HOH A 26 1026 90 HOH HOH . D 4 HOH A 27 1027 289 HOH HOH . D 4 HOH A 28 1028 91 HOH HOH . D 4 HOH A 29 1029 191 HOH HOH . D 4 HOH A 30 1030 120 HOH HOH . D 4 HOH A 31 1031 34 HOH HOH . D 4 HOH A 32 1032 63 HOH HOH . D 4 HOH A 33 1033 177 HOH HOH . D 4 HOH A 34 1034 123 HOH HOH . D 4 HOH A 35 1035 92 HOH HOH . D 4 HOH A 36 1036 12 HOH HOH . D 4 HOH A 37 1037 255 HOH HOH . D 4 HOH A 38 1038 4 HOH HOH . D 4 HOH A 39 1039 30 HOH HOH . D 4 HOH A 40 1040 282 HOH HOH . D 4 HOH A 41 1041 103 HOH HOH . D 4 HOH A 42 1042 78 HOH HOH . D 4 HOH A 43 1043 131 HOH HOH . D 4 HOH A 44 1044 263 HOH HOH . D 4 HOH A 45 1045 190 HOH HOH . D 4 HOH A 46 1046 25 HOH HOH . D 4 HOH A 47 1047 50 HOH HOH . D 4 HOH A 48 1048 89 HOH HOH . D 4 HOH A 49 1049 192 HOH HOH . D 4 HOH A 50 1050 104 HOH HOH . D 4 HOH A 51 1051 267 HOH HOH . D 4 HOH A 52 1052 19 HOH HOH . D 4 HOH A 53 1053 105 HOH HOH . D 4 HOH A 54 1054 13 HOH HOH . D 4 HOH A 55 1055 106 HOH HOH . D 4 HOH A 56 1056 280 HOH HOH . D 4 HOH A 57 1057 28 HOH HOH . D 4 HOH A 58 1058 254 HOH HOH . D 4 HOH A 59 1059 133 HOH HOH . D 4 HOH A 60 1060 72 HOH HOH . D 4 HOH A 61 1061 23 HOH HOH . D 4 HOH A 62 1062 150 HOH HOH . D 4 HOH A 63 1063 40 HOH HOH . D 4 HOH A 64 1064 176 HOH HOH . D 4 HOH A 65 1065 224 HOH HOH . D 4 HOH A 66 1066 127 HOH HOH . D 4 HOH A 67 1067 121 HOH HOH . D 4 HOH A 68 1068 142 HOH HOH . D 4 HOH A 69 1069 31 HOH HOH . D 4 HOH A 70 1070 297 HOH HOH . D 4 HOH A 71 1071 24 HOH HOH . D 4 HOH A 72 1072 7 HOH HOH . D 4 HOH A 73 1073 99 HOH HOH . D 4 HOH A 74 1074 81 HOH HOH . D 4 HOH A 75 1075 235 HOH HOH . D 4 HOH A 76 1076 128 HOH HOH . D 4 HOH A 77 1077 67 HOH HOH . D 4 HOH A 78 1078 111 HOH HOH . D 4 HOH A 79 1079 62 HOH HOH . D 4 HOH A 80 1080 172 HOH HOH . D 4 HOH A 81 1081 129 HOH HOH . D 4 HOH A 82 1082 307 HOH HOH . D 4 HOH A 83 1083 117 HOH HOH . D 4 HOH A 84 1084 174 HOH HOH . D 4 HOH A 85 1085 153 HOH HOH . D 4 HOH A 86 1086 306 HOH HOH . D 4 HOH A 87 1087 44 HOH HOH . D 4 HOH A 88 1088 284 HOH HOH . D 4 HOH A 89 1089 302 HOH HOH . D 4 HOH A 90 1090 76 HOH HOH . D 4 HOH A 91 1091 132 HOH HOH . D 4 HOH A 92 1092 213 HOH HOH . D 4 HOH A 93 1093 276 HOH HOH . D 4 HOH A 94 1094 114 HOH HOH . D 4 HOH A 95 1095 161 HOH HOH . D 4 HOH A 96 1096 163 HOH HOH . D 4 HOH A 97 1097 262 HOH HOH . D 4 HOH A 98 1098 71 HOH HOH . D 4 HOH A 99 1099 266 HOH HOH . D 4 HOH A 100 1100 38 HOH HOH . D 4 HOH A 101 1101 94 HOH HOH . D 4 HOH A 102 1102 112 HOH HOH . D 4 HOH A 103 1103 22 HOH HOH . D 4 HOH A 104 1104 85 HOH HOH . D 4 HOH A 105 1105 178 HOH HOH . D 4 HOH A 106 1106 14 HOH HOH . D 4 HOH A 107 1107 145 HOH HOH . D 4 HOH A 108 1108 179 HOH HOH . D 4 HOH A 109 1109 175 HOH HOH . D 4 HOH A 110 1110 49 HOH HOH . D 4 HOH A 111 1111 42 HOH HOH . D 4 HOH A 112 1112 88 HOH HOH . D 4 HOH A 113 1113 41 HOH HOH . D 4 HOH A 114 1114 83 HOH HOH . D 4 HOH A 115 1115 82 HOH HOH . D 4 HOH A 116 1116 275 HOH HOH . D 4 HOH A 117 1117 293 HOH HOH . D 4 HOH A 118 1118 27 HOH HOH . D 4 HOH A 119 1119 152 HOH HOH . D 4 HOH A 120 1120 180 HOH HOH . D 4 HOH A 121 1121 56 HOH HOH . D 4 HOH A 122 1122 277 HOH HOH . D 4 HOH A 123 1123 115 HOH HOH . D 4 HOH A 124 1124 57 HOH HOH . D 4 HOH A 125 1125 55 HOH HOH . D 4 HOH A 126 1126 9 HOH HOH . D 4 HOH A 127 1127 11 HOH HOH . D 4 HOH A 128 1128 45 HOH HOH . D 4 HOH A 129 1129 140 HOH HOH . D 4 HOH A 130 1130 80 HOH HOH . D 4 HOH A 131 1131 160 HOH HOH . D 4 HOH A 132 1132 149 HOH HOH . D 4 HOH A 133 1133 155 HOH HOH . D 4 HOH A 134 1134 33 HOH HOH . D 4 HOH A 135 1135 157 HOH HOH . D 4 HOH A 136 1136 43 HOH HOH . D 4 HOH A 137 1137 151 HOH HOH . D 4 HOH A 138 1138 87 HOH HOH . D 4 HOH A 139 1139 141 HOH HOH . D 4 HOH A 140 1140 95 HOH HOH . D 4 HOH A 141 1141 259 HOH HOH . D 4 HOH A 142 1142 162 HOH HOH . D 4 HOH A 143 1143 54 HOH HOH . D 4 HOH A 144 1144 21 HOH HOH . D 4 HOH A 145 1145 184 HOH HOH . D 4 HOH A 146 1146 216 HOH HOH . D 4 HOH A 147 1147 290 HOH HOH . D 4 HOH A 148 1148 97 HOH HOH . D 4 HOH A 149 1149 234 HOH HOH . D 4 HOH A 150 1150 237 HOH HOH . D 4 HOH A 151 1151 93 HOH HOH . D 4 HOH A 152 1152 271 HOH HOH . D 4 HOH A 153 1153 294 HOH HOH . D 4 HOH A 154 1154 3 HOH HOH . D 4 HOH A 155 1155 5 HOH HOH . D 4 HOH A 156 1156 274 HOH HOH . D 4 HOH A 157 1157 51 HOH HOH . D 4 HOH A 158 1158 251 HOH HOH . D 4 HOH A 159 1159 212 HOH HOH . D 4 HOH A 160 1160 261 HOH HOH . D 4 HOH A 161 1161 2 HOH HOH . D 4 HOH A 162 1162 303 HOH HOH . D 4 HOH A 163 1163 270 HOH HOH . D 4 HOH A 164 1164 278 HOH HOH . D 4 HOH A 165 1165 189 HOH HOH . D 4 HOH A 166 1166 35 HOH HOH . D 4 HOH A 167 1167 248 HOH HOH . D 4 HOH A 168 1168 60 HOH HOH . D 4 HOH A 169 1169 279 HOH HOH . D 4 HOH A 170 1170 236 HOH HOH . D 4 HOH A 171 1171 249 HOH HOH . D 4 HOH A 172 1172 291 HOH HOH . D 4 HOH A 173 1173 273 HOH HOH . D 4 HOH A 174 1174 193 HOH HOH . D 4 HOH A 175 1175 288 HOH HOH . D 4 HOH A 176 1176 299 HOH HOH . D 4 HOH A 177 1177 16 HOH HOH . D 4 HOH A 178 1178 164 HOH HOH . D 4 HOH A 179 1179 304 HOH HOH . D 4 HOH A 180 1180 242 HOH HOH . D 4 HOH A 181 1181 268 HOH HOH . D 4 HOH A 182 1182 308 HOH HOH . D 4 HOH A 183 1183 143 HOH HOH . D 4 HOH A 184 1184 265 HOH HOH . D 4 HOH A 185 1185 245 HOH HOH . D 4 HOH A 186 1186 296 HOH HOH . D 4 HOH A 187 1187 295 HOH HOH . D 4 HOH A 188 1188 285 HOH HOH . D 4 HOH A 189 1189 281 HOH HOH . D 4 HOH A 190 1190 250 HOH HOH . D 4 HOH A 191 1191 70 HOH HOH . D 4 HOH A 192 1192 247 HOH HOH . D 4 HOH A 193 1193 309 HOH HOH . D 4 HOH A 194 1194 264 HOH HOH . D 4 HOH A 195 1195 287 HOH HOH . D 4 HOH A 196 1196 244 HOH HOH . D 4 HOH A 197 1197 256 HOH HOH . D 4 HOH A 198 1198 253 HOH HOH . D 4 HOH A 199 1199 257 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 24.715 25.562 30.25 1 13.72 ? N1 PLP 901 A 1 HETATM 2 C C2 PLP . . . B 2 23.595 24.861 30.482 1 13.31 ? C2 PLP 901 A 1 HETATM 3 C C2A PLP . . . B 2 22.668 25.368 31.52 1 13.01 ? C2A PLP 901 A 1 HETATM 4 C C3 PLP . . . B 2 23.318 23.632 29.714 1 13.79 ? C3 PLP 901 A 1 HETATM 5 O O3 PLP . . . B 2 22.154 22.885 29.904 1 14.7 ? O3 PLP 901 A 1 HETATM 6 C C4 PLP . . . B 2 24.268 23.313 28.659 1 13.36 ? C4 PLP 901 A 1 HETATM 7 C C4A PLP . . . B 2 24.081 22.075 27.793 1 14.46 ? C4A PLP 901 A 1 HETATM 8 C C5 PLP . . . B 2 25.444 24.184 28.497 1 13.38 ? C5 PLP 901 A 1 HETATM 9 C C6 PLP . . . B 2 25.644 25.288 29.316 1 13.42 ? C6 PLP 901 A 1 HETATM 10 C C5A PLP . . . B 2 26.529 23.935 27.463 1 13.04 ? C5A PLP 901 A 1 HETATM 11 O O4P PLP . . . B 2 26.043 24.574 26.35 1 12.44 ? O4P PLP 901 A 1 HETATM 12 P P PLP . . . B 2 27.005 24.861 25.086 1 13.46 ? P PLP 901 A 1 HETATM 13 O O1P PLP . . . B 2 26.058 25.344 24.06 1 12.72 ? O1P PLP 901 A 1 HETATM 14 O O2P PLP . . . B 2 28.01 25.946 25.535 1 13.13 ? O2P PLP 901 A 1 HETATM 15 O O3P PLP . . . B 2 27.669 23.52 24.717 1 13.32 ? O3P PLP 901 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 15 #