data_1C8V # _model_server_result.job_id VVbBTPmfRY3Qb9nQe01lew _model_server_result.datetime_utc '2025-02-26 14:59:59' _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 1c8v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":900}' # _entry.id 1C8V # _exptl.entry_id 1C8V _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'metal cofactor bound at the beta subunit' _entity.formula_weight 247.142 _entity.id 5 _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 94.38 _cell.angle_gamma 90 _cell.entry_id 1C8V _cell.length_a 183.8 _cell.length_b 60.77 _cell.length_c 68.15 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1C8V _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 183.8 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 B NZ LYS 87 B LYS 87 1_555 E C4A PLP . B PLP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? metalc ? metalc1 B O GLY 232 B GLY 232 1_555 D NA NA . B NA 1169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 B O PHE 306 B PHE 306 1_555 D NA NA . B NA 1169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc3 B O SER 308 B SER 308 1_555 D NA NA . B NA 1169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc4 G O HOH . B HOH 1029 1_555 D NA NA . B NA 1169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc5 G O HOH . B HOH 1159 1_555 D NA NA . B NA 1169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? # _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 289 n y N1 C6 PLP sing 290 n y C2 C2A PLP sing 291 n n C2 C3 PLP sing 292 n y C2A H2A1 PLP sing 293 n n C2A H2A2 PLP sing 294 n n C2A H2A3 PLP sing 295 n n C3 O3 PLP sing 296 n n C3 C4 PLP doub 297 n y O3 HO3 PLP sing 298 n n C4 C4A PLP sing 299 n n C4 C5 PLP sing 300 n y C4A O4A PLP doub 301 n n C4A H4A PLP sing 302 n n C5 C6 PLP doub 303 n y C5 C5A PLP sing 304 n n C6 H6 PLP sing 305 n n C5A O4P PLP sing 306 n n C5A H5A1 PLP sing 307 n n C5A H5A2 PLP sing 308 n n O4P P PLP sing 309 n n P O1P PLP doub 310 n n P O2P PLP sing 311 n n P O3P PLP sing 312 n n O2P HOP2 PLP sing 313 n n O3P HOP3 PLP sing 314 n n # _atom_sites.entry_id 1C8V _atom_sites.fract_transf_matrix[1][1] 0.005441 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000417 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016455 _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] 0.014716 _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 3 HE1 A 1 270 270 HE1 HE1 . D 4 NA B 1 1169 1169 NA NA . E 5 PLP B 1 900 900 PLP PLP . F 6 HOH A 1 1002 1002 HOH HOH . F 6 HOH A 2 1003 1003 HOH HOH . F 6 HOH A 3 1005 1005 HOH HOH . F 6 HOH A 4 1010 1010 HOH HOH . F 6 HOH A 5 1018 1018 HOH HOH . F 6 HOH A 6 1020 1020 HOH HOH . F 6 HOH A 7 1025 1025 HOH HOH . F 6 HOH A 8 1032 1032 HOH HOH . F 6 HOH A 9 1033 1033 HOH HOH . F 6 HOH A 10 1036 1036 HOH HOH . F 6 HOH A 11 1039 1039 HOH HOH . F 6 HOH A 12 1041 1041 HOH HOH . F 6 HOH A 13 1042 1042 HOH HOH . F 6 HOH A 14 1045 1045 HOH HOH . F 6 HOH A 15 1050 1050 HOH HOH . F 6 HOH A 16 1054 1054 HOH HOH . F 6 HOH A 17 1056 1056 HOH HOH . F 6 HOH A 18 1058 1058 HOH HOH . F 6 HOH A 19 1059 1059 HOH HOH . F 6 HOH A 20 1062 1062 HOH HOH . F 6 HOH A 21 1064 1064 HOH HOH . F 6 HOH A 22 1065 1065 HOH HOH . F 6 HOH A 23 1070 1070 HOH HOH . F 6 HOH A 24 1074 1074 HOH HOH . F 6 HOH A 25 1077 1077 HOH HOH . F 6 HOH A 26 1078 1078 HOH HOH . F 6 HOH A 27 1079 1079 HOH HOH . F 6 HOH A 28 1084 1084 HOH HOH . F 6 HOH A 29 1087 1087 HOH HOH . F 6 HOH A 30 1088 1088 HOH HOH . F 6 HOH A 31 1089 1089 HOH HOH . F 6 HOH A 32 1090 1090 HOH HOH . F 6 HOH A 33 1092 1092 HOH HOH . F 6 HOH A 34 1093 1093 HOH HOH . F 6 HOH A 35 1096 1096 HOH HOH . F 6 HOH A 36 1099 1099 HOH HOH . F 6 HOH A 37 1100 1100 HOH HOH . F 6 HOH A 38 1102 1102 HOH HOH . F 6 HOH A 39 1106 1106 HOH HOH . F 6 HOH A 40 1107 1107 HOH HOH . F 6 HOH A 41 1108 1108 HOH HOH . F 6 HOH A 42 1113 1113 HOH HOH . F 6 HOH A 43 1115 1115 HOH HOH . F 6 HOH A 44 1117 1117 HOH HOH . F 6 HOH A 45 1122 1122 HOH HOH . F 6 HOH A 46 1123 1123 HOH HOH . F 6 HOH A 47 1128 1128 HOH HOH . F 6 HOH A 48 1131 1131 HOH HOH . F 6 HOH A 49 1132 1132 HOH HOH . F 6 HOH A 50 1144 1144 HOH HOH . F 6 HOH A 51 1147 1147 HOH HOH . F 6 HOH A 52 1148 1148 HOH HOH . F 6 HOH A 53 1150 1150 HOH HOH . F 6 HOH A 54 1151 1151 HOH HOH . F 6 HOH A 55 1153 1153 HOH HOH . F 6 HOH A 56 1154 1154 HOH HOH . F 6 HOH A 57 1157 1157 HOH HOH . F 6 HOH A 58 1161 1161 HOH HOH . F 6 HOH A 59 1162 1162 HOH HOH . F 6 HOH A 60 1164 1164 HOH HOH . F 6 HOH A 61 1166 1166 HOH HOH . G 6 HOH B 1 1001 1001 HOH HOH . G 6 HOH B 2 1004 1004 HOH HOH . G 6 HOH B 3 1006 1006 HOH HOH . G 6 HOH B 4 1007 1007 HOH HOH . G 6 HOH B 5 1008 1008 HOH HOH . G 6 HOH B 6 1009 1009 HOH HOH . G 6 HOH B 7 1011 1011 HOH HOH . G 6 HOH B 8 1012 1012 HOH HOH . G 6 HOH B 9 1013 1013 HOH HOH . G 6 HOH B 10 1014 1014 HOH HOH . G 6 HOH B 11 1015 1015 HOH HOH . G 6 HOH B 12 1016 1016 HOH HOH . G 6 HOH B 13 1017 1017 HOH HOH . G 6 HOH B 14 1019 1019 HOH HOH . G 6 HOH B 15 1021 1021 HOH HOH . G 6 HOH B 16 1022 1022 HOH HOH . G 6 HOH B 17 1023 1023 HOH HOH . G 6 HOH B 18 1024 1024 HOH HOH . G 6 HOH B 19 1026 1026 HOH HOH . G 6 HOH B 20 1027 1027 HOH HOH . G 6 HOH B 21 1028 1028 HOH HOH . G 6 HOH B 22 1029 1029 HOH HOH . G 6 HOH B 23 1030 1030 HOH HOH . G 6 HOH B 24 1031 1031 HOH HOH . G 6 HOH B 25 1034 1034 HOH HOH . G 6 HOH B 26 1035 1035 HOH HOH . G 6 HOH B 27 1037 1037 HOH HOH . G 6 HOH B 28 1038 1038 HOH HOH . G 6 HOH B 29 1040 1040 HOH HOH . G 6 HOH B 30 1043 1043 HOH HOH . G 6 HOH B 31 1044 1044 HOH HOH . G 6 HOH B 32 1047 1047 HOH HOH . G 6 HOH B 33 1048 1048 HOH HOH . G 6 HOH B 34 1049 1049 HOH HOH . G 6 HOH B 35 1051 1051 HOH HOH . G 6 HOH B 36 1052 1052 HOH HOH . G 6 HOH B 37 1053 1053 HOH HOH . G 6 HOH B 38 1055 1055 HOH HOH . G 6 HOH B 39 1057 1057 HOH HOH . G 6 HOH B 40 1060 1060 HOH HOH . G 6 HOH B 41 1061 1061 HOH HOH . G 6 HOH B 42 1063 1063 HOH HOH . G 6 HOH B 43 1066 1066 HOH HOH . G 6 HOH B 44 1068 1068 HOH HOH . G 6 HOH B 45 1069 1069 HOH HOH . G 6 HOH B 46 1071 1071 HOH HOH . G 6 HOH B 47 1072 1072 HOH HOH . G 6 HOH B 48 1073 1073 HOH HOH . G 6 HOH B 49 1075 1075 HOH HOH . G 6 HOH B 50 1076 1076 HOH HOH . G 6 HOH B 51 1080 1080 HOH HOH . G 6 HOH B 52 1081 1081 HOH HOH . G 6 HOH B 53 1082 1082 HOH HOH . G 6 HOH B 54 1083 1083 HOH HOH . G 6 HOH B 55 1085 1085 HOH HOH . G 6 HOH B 56 1086 1086 HOH HOH . G 6 HOH B 57 1091 1091 HOH HOH . G 6 HOH B 58 1095 1095 HOH HOH . G 6 HOH B 59 1097 1097 HOH HOH . G 6 HOH B 60 1103 1103 HOH HOH . G 6 HOH B 61 1104 1104 HOH HOH . G 6 HOH B 62 1105 1105 HOH HOH . G 6 HOH B 63 1110 1110 HOH HOH . G 6 HOH B 64 1111 1111 HOH HOH . G 6 HOH B 65 1112 1112 HOH HOH . G 6 HOH B 66 1114 1114 HOH HOH . G 6 HOH B 67 1116 1116 HOH HOH . G 6 HOH B 68 1118 1118 HOH HOH . G 6 HOH B 69 1119 1119 HOH HOH . G 6 HOH B 70 1120 1120 HOH HOH . G 6 HOH B 71 1121 1121 HOH HOH . G 6 HOH B 72 1124 1124 HOH HOH . G 6 HOH B 73 1126 1126 HOH HOH . G 6 HOH B 74 1127 1127 HOH HOH . G 6 HOH B 75 1129 1129 HOH HOH . G 6 HOH B 76 1130 1130 HOH HOH . G 6 HOH B 77 1133 1133 HOH HOH . G 6 HOH B 78 1134 1134 HOH HOH . G 6 HOH B 79 1135 1135 HOH HOH . G 6 HOH B 80 1136 1136 HOH HOH . G 6 HOH B 81 1137 1137 HOH HOH . G 6 HOH B 82 1138 1138 HOH HOH . G 6 HOH B 83 1139 1139 HOH HOH . G 6 HOH B 84 1140 1140 HOH HOH . G 6 HOH B 85 1141 1141 HOH HOH . G 6 HOH B 86 1142 1142 HOH HOH . G 6 HOH B 87 1143 1143 HOH HOH . G 6 HOH B 88 1145 1145 HOH HOH . G 6 HOH B 89 1146 1146 HOH HOH . G 6 HOH B 90 1149 1149 HOH HOH . G 6 HOH B 91 1152 1152 HOH HOH . G 6 HOH B 92 1155 1155 HOH HOH . G 6 HOH B 93 1156 1156 HOH HOH . G 6 HOH B 94 1158 1158 HOH HOH . G 6 HOH B 95 1159 1159 HOH HOH . G 6 HOH B 96 1160 1160 HOH HOH . G 6 HOH B 97 1163 1163 HOH HOH . G 6 HOH B 98 1165 1165 HOH HOH . G 6 HOH B 99 1167 1167 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 . . . E 5 84.899 13.856 12.066 1 8.82 ? N1 PLP 900 B 1 HETATM 2 C C2 PLP . . . E 5 84.937 14.217 10.755 1 13.98 ? C2 PLP 900 B 1 HETATM 3 C C2A PLP . . . E 5 86.223 14.078 9.998 1 6.53 ? C2A PLP 900 B 1 HETATM 4 C C3 PLP . . . E 5 83.765 14.709 10.171 1 13.99 ? C3 PLP 900 B 1 HETATM 5 O O3 PLP . . . E 5 83.871 15.059 8.819 1 17.68 ? O3 PLP 900 B 1 HETATM 6 C C4 PLP . . . E 5 82.523 14.861 10.833 1 19.68 ? C4 PLP 900 B 1 HETATM 7 C C4A PLP . . . E 5 81.522 14.894 9.794 1 22.05 ? C4A PLP 900 B 1 HETATM 8 C C5 PLP . . . E 5 82.581 14.5 12.194 1 17.68 ? C5 PLP 900 B 1 HETATM 9 C C6 PLP . . . E 5 83.733 14.016 12.728 1 15.03 ? C6 PLP 900 B 1 HETATM 10 C C5A PLP . . . E 5 81.418 14.691 13.231 1 15.19 ? C5A PLP 900 B 1 HETATM 11 O O4P PLP . . . E 5 80.972 13.448 13.533 1 16.72 ? O4P PLP 900 B 1 HETATM 12 P P PLP . . . E 5 80.004 12.398 14.062 1 13.53 ? P PLP 900 B 1 HETATM 13 O O1P PLP . . . E 5 78.671 12.167 13.479 1 11.45 ? O1P PLP 900 B 1 HETATM 14 O O2P PLP . . . E 5 80.691 11.149 13.8 1 15.07 ? O2P PLP 900 B 1 HETATM 15 O O3P PLP . . . E 5 79.975 12.631 15.509 1 7.65 ? O3P PLP 900 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 15 #