data_1KTA # _model_server_result.job_id USc-XdeWG8BZvs1Prkzpjg _model_server_result.datetime_utc '2024-12-03 10:21:38' _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 1kta # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 1KTA # _exptl.entry_id 1KTA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.173 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 1KTA _cell.length_a 69.45 _cell.length_b 105.308 _cell.length_c 107.829 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KTA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,E,F,G,H,I,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 2 C N N ? 2 H N N # _chem_comp.formula 'C8 H13 N2 O5 P' _chem_comp.formula_weight 248.173 _chem_comp.id PMP _chem_comp.mon_nstd_flag . _chem_comp.name "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "PYRIDOXAMINE-5'-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 PMP doub 295 n y N1 C6 PMP sing 296 n y C2 C2A PMP sing 297 n n C2 C3 PMP sing 298 n y C2A H2A1 PMP sing 299 n n C2A H2A2 PMP sing 300 n n C2A H2A3 PMP sing 301 n n C3 O3 PMP sing 302 n n C3 C4 PMP doub 303 n y O3 HO3 PMP sing 304 n n C4 C4A PMP sing 305 n n C4 C5 PMP sing 306 n y C4A N4A PMP sing 307 n n C4A H4A1 PMP sing 308 n n C4A H4A2 PMP sing 309 n n N4A HNA1 PMP sing 310 n n N4A HNA2 PMP sing 311 n n C5 C6 PMP doub 312 n y C5 C5A PMP sing 313 n n C6 H6 PMP sing 314 n n C5A O4P PMP sing 315 n n C5A H5A1 PMP sing 316 n n C5A H5A2 PMP sing 317 n n O4P P PMP sing 318 n n P O1P PMP doub 319 n n P O2P PMP sing 320 n n P O3P PMP sing 321 n n O2P HOP2 PMP sing 322 n n O3P HOP3 PMP sing 323 n n # _atom_sites.entry_id 1KTA _atom_sites.fract_transf_matrix[1][1] 0.014399 _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] 0.009496 _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] 0.009274 _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 PMP A 1 400 400 PMP PMP . D 3 ACY A 1 1003 1003 ACY ACY . E 3 ACY A 1 1006 1006 ACY ACY . F 3 ACY A 1 1007 1007 ACY ACY . G 4 KIV B 1 3001 3001 KIV KIV . H 2 PMP B 1 900 900 PMP PMP . I 3 ACY B 1 1001 1001 ACY ACY . J 3 ACY B 1 1002 1002 ACY ACY . K 3 ACY B 1 1004 1004 ACY ACY . L 3 ACY B 1 1005 1005 ACY ACY . M 5 GOL B 1 2001 2001 GOL GOL . N 6 HOH A 1 1008 1 HOH HOH . N 6 HOH A 2 1009 4 HOH HOH . N 6 HOH A 3 1010 5 HOH HOH . N 6 HOH A 4 1011 8 HOH HOH . N 6 HOH A 5 1012 9 HOH HOH . N 6 HOH A 6 1013 11 HOH HOH . N 6 HOH A 7 1014 13 HOH HOH . N 6 HOH A 8 1015 15 HOH HOH . N 6 HOH A 9 1016 16 HOH HOH . N 6 HOH A 10 1017 17 HOH HOH . N 6 HOH A 11 1018 18 HOH HOH . N 6 HOH A 12 1019 20 HOH HOH . N 6 HOH A 13 1020 27 HOH HOH . N 6 HOH A 14 1021 29 HOH HOH . N 6 HOH A 15 1022 30 HOH HOH . N 6 HOH A 16 1023 31 HOH HOH . N 6 HOH A 17 1024 34 HOH HOH . N 6 HOH A 18 1025 37 HOH HOH . N 6 HOH A 19 1026 38 HOH HOH . N 6 HOH A 20 1027 39 HOH HOH . N 6 HOH A 21 1028 41 HOH HOH . N 6 HOH A 22 1029 43 HOH HOH . N 6 HOH A 23 1030 48 HOH HOH . N 6 HOH A 24 1031 49 HOH HOH . N 6 HOH A 25 1032 50 HOH HOH . N 6 HOH A 26 1033 51 HOH HOH . N 6 HOH A 27 1034 53 HOH HOH . N 6 HOH A 28 1035 54 HOH HOH . N 6 HOH A 29 1036 57 HOH HOH . N 6 HOH A 30 1037 58 HOH HOH . N 6 HOH A 31 1038 59 HOH HOH . N 6 HOH A 32 1039 60 HOH HOH . N 6 HOH A 33 1040 61 HOH HOH . N 6 HOH A 34 1041 63 HOH HOH . N 6 HOH A 35 1042 65 HOH HOH . N 6 HOH A 36 1043 67 HOH HOH . N 6 HOH A 37 1044 68 HOH HOH . N 6 HOH A 38 1045 69 HOH HOH . N 6 HOH A 39 1046 70 HOH HOH . N 6 HOH A 40 1047 74 HOH HOH . N 6 HOH A 41 1048 76 HOH HOH . N 6 HOH A 42 1049 79 HOH HOH . N 6 HOH A 43 1050 80 HOH HOH . N 6 HOH A 44 1051 81 HOH HOH . N 6 HOH A 45 1052 82 HOH HOH . N 6 HOH A 46 1053 84 HOH HOH . N 6 HOH A 47 1054 87 HOH HOH . N 6 HOH A 48 1055 88 HOH HOH . N 6 HOH A 49 1056 90 HOH HOH . N 6 HOH A 50 1057 91 HOH HOH . N 6 HOH A 51 1058 93 HOH HOH . N 6 HOH A 52 1059 95 HOH HOH . N 6 HOH A 53 1060 97 HOH HOH . N 6 HOH A 54 1061 99 HOH HOH . N 6 HOH A 55 1062 101 HOH HOH . N 6 HOH A 56 1063 105 HOH HOH . N 6 HOH A 57 1064 106 HOH HOH . N 6 HOH A 58 1065 107 HOH HOH . N 6 HOH A 59 1066 108 HOH HOH . N 6 HOH A 60 1067 112 HOH HOH . N 6 HOH A 61 1068 113 HOH HOH . N 6 HOH A 62 1069 115 HOH HOH . N 6 HOH A 63 1070 119 HOH HOH . N 6 HOH A 64 1071 121 HOH HOH . N 6 HOH A 65 1072 122 HOH HOH . N 6 HOH A 66 1073 125 HOH HOH . N 6 HOH A 67 1074 127 HOH HOH . N 6 HOH A 68 1075 128 HOH HOH . N 6 HOH A 69 1076 131 HOH HOH . N 6 HOH A 70 1077 133 HOH HOH . N 6 HOH A 71 1078 135 HOH HOH . N 6 HOH A 72 1079 137 HOH HOH . N 6 HOH A 73 1080 140 HOH HOH . N 6 HOH A 74 1081 141 HOH HOH . N 6 HOH A 75 1082 143 HOH HOH . N 6 HOH A 76 1083 144 HOH HOH . N 6 HOH A 77 1084 146 HOH HOH . N 6 HOH A 78 1085 147 HOH HOH . N 6 HOH A 79 1086 148 HOH HOH . N 6 HOH A 80 1087 155 HOH HOH . N 6 HOH A 81 1088 156 HOH HOH . N 6 HOH A 82 1089 158 HOH HOH . N 6 HOH A 83 1090 160 HOH HOH . N 6 HOH A 84 1091 164 HOH HOH . N 6 HOH A 85 1092 167 HOH HOH . N 6 HOH A 86 1093 168 HOH HOH . N 6 HOH A 87 1094 170 HOH HOH . N 6 HOH A 88 1095 171 HOH HOH . N 6 HOH A 89 1096 174 HOH HOH . N 6 HOH A 90 1097 176 HOH HOH . N 6 HOH A 91 1098 177 HOH HOH . N 6 HOH A 92 1099 178 HOH HOH . N 6 HOH A 93 1100 183 HOH HOH . N 6 HOH A 94 1101 184 HOH HOH . N 6 HOH A 95 1102 186 HOH HOH . N 6 HOH A 96 1103 188 HOH HOH . N 6 HOH A 97 1104 190 HOH HOH . N 6 HOH A 98 1105 191 HOH HOH . N 6 HOH A 99 1106 195 HOH HOH . N 6 HOH A 100 1107 196 HOH HOH . N 6 HOH A 101 1108 197 HOH HOH . N 6 HOH A 102 1109 202 HOH HOH . N 6 HOH A 103 1110 203 HOH HOH . N 6 HOH A 104 1111 204 HOH HOH . N 6 HOH A 105 1112 205 HOH HOH . N 6 HOH A 106 1113 206 HOH HOH . N 6 HOH A 107 1114 208 HOH HOH . N 6 HOH A 108 1115 210 HOH HOH . N 6 HOH A 109 1116 211 HOH HOH . N 6 HOH A 110 1117 213 HOH HOH . N 6 HOH A 111 1118 214 HOH HOH . N 6 HOH A 112 1119 216 HOH HOH . N 6 HOH A 113 1120 219 HOH HOH . N 6 HOH A 114 1121 220 HOH HOH . N 6 HOH A 115 1122 221 HOH HOH . N 6 HOH A 116 1123 222 HOH HOH . N 6 HOH A 117 1124 223 HOH HOH . N 6 HOH A 118 1125 225 HOH HOH . N 6 HOH A 119 1126 227 HOH HOH . N 6 HOH A 120 1127 228 HOH HOH . N 6 HOH A 121 1128 230 HOH HOH . N 6 HOH A 122 1129 231 HOH HOH . N 6 HOH A 123 1130 232 HOH HOH . N 6 HOH A 124 1131 234 HOH HOH . N 6 HOH A 125 1132 236 HOH HOH . N 6 HOH A 126 1133 238 HOH HOH . O 6 HOH B 1 2 2 HOH HOH . O 6 HOH B 2 3 3 HOH HOH . O 6 HOH B 3 6 6 HOH HOH . O 6 HOH B 4 7 7 HOH HOH . O 6 HOH B 5 10 10 HOH HOH . O 6 HOH B 6 12 12 HOH HOH . O 6 HOH B 7 14 14 HOH HOH . O 6 HOH B 8 19 19 HOH HOH . O 6 HOH B 9 21 21 HOH HOH . O 6 HOH B 10 22 22 HOH HOH . O 6 HOH B 11 23 23 HOH HOH . O 6 HOH B 12 24 24 HOH HOH . O 6 HOH B 13 25 25 HOH HOH . O 6 HOH B 14 26 26 HOH HOH . O 6 HOH B 15 28 28 HOH HOH . O 6 HOH B 16 32 32 HOH HOH . O 6 HOH B 17 33 33 HOH HOH . O 6 HOH B 18 35 35 HOH HOH . O 6 HOH B 19 36 36 HOH HOH . O 6 HOH B 20 40 40 HOH HOH . O 6 HOH B 21 42 42 HOH HOH . O 6 HOH B 22 44 44 HOH HOH . O 6 HOH B 23 45 45 HOH HOH . O 6 HOH B 24 46 46 HOH HOH . O 6 HOH B 25 47 47 HOH HOH . O 6 HOH B 26 52 52 HOH HOH . O 6 HOH B 27 55 55 HOH HOH . O 6 HOH B 28 56 56 HOH HOH . O 6 HOH B 29 62 62 HOH HOH . O 6 HOH B 30 64 64 HOH HOH . O 6 HOH B 31 66 66 HOH HOH . O 6 HOH B 32 71 71 HOH HOH . O 6 HOH B 33 72 72 HOH HOH . O 6 HOH B 34 73 73 HOH HOH . O 6 HOH B 35 75 75 HOH HOH . O 6 HOH B 36 77 77 HOH HOH . O 6 HOH B 37 78 78 HOH HOH . O 6 HOH B 38 83 83 HOH HOH . O 6 HOH B 39 85 85 HOH HOH . O 6 HOH B 40 86 86 HOH HOH . O 6 HOH B 41 89 89 HOH HOH . O 6 HOH B 42 92 92 HOH HOH . O 6 HOH B 43 94 94 HOH HOH . O 6 HOH B 44 96 96 HOH HOH . O 6 HOH B 45 98 98 HOH HOH . O 6 HOH B 46 100 100 HOH HOH . O 6 HOH B 47 102 102 HOH HOH . O 6 HOH B 48 103 103 HOH HOH . O 6 HOH B 49 104 104 HOH HOH . O 6 HOH B 50 109 109 HOH HOH . O 6 HOH B 51 110 110 HOH HOH . O 6 HOH B 52 111 111 HOH HOH . O 6 HOH B 53 114 114 HOH HOH . O 6 HOH B 54 116 116 HOH HOH . O 6 HOH B 55 117 117 HOH HOH . O 6 HOH B 56 118 118 HOH HOH . O 6 HOH B 57 120 120 HOH HOH . O 6 HOH B 58 123 123 HOH HOH . O 6 HOH B 59 124 124 HOH HOH . O 6 HOH B 60 126 126 HOH HOH . O 6 HOH B 61 129 129 HOH HOH . O 6 HOH B 62 130 130 HOH HOH . O 6 HOH B 63 132 132 HOH HOH . O 6 HOH B 64 134 134 HOH HOH . O 6 HOH B 65 136 136 HOH HOH . O 6 HOH B 66 138 138 HOH HOH . O 6 HOH B 67 139 139 HOH HOH . O 6 HOH B 68 142 142 HOH HOH . O 6 HOH B 69 145 145 HOH HOH . O 6 HOH B 70 149 149 HOH HOH . O 6 HOH B 71 150 150 HOH HOH . O 6 HOH B 72 151 151 HOH HOH . O 6 HOH B 73 152 152 HOH HOH . O 6 HOH B 74 153 153 HOH HOH . O 6 HOH B 75 154 154 HOH HOH . O 6 HOH B 76 157 157 HOH HOH . O 6 HOH B 77 159 159 HOH HOH . O 6 HOH B 78 161 161 HOH HOH . O 6 HOH B 79 162 162 HOH HOH . O 6 HOH B 80 163 163 HOH HOH . O 6 HOH B 81 165 165 HOH HOH . O 6 HOH B 82 166 166 HOH HOH . O 6 HOH B 83 169 169 HOH HOH . O 6 HOH B 84 172 172 HOH HOH . O 6 HOH B 85 173 173 HOH HOH . O 6 HOH B 86 175 175 HOH HOH . O 6 HOH B 87 179 179 HOH HOH . O 6 HOH B 88 180 180 HOH HOH . O 6 HOH B 89 181 181 HOH HOH . O 6 HOH B 90 182 182 HOH HOH . O 6 HOH B 91 185 185 HOH HOH . O 6 HOH B 92 187 187 HOH HOH . O 6 HOH B 93 189 189 HOH HOH . O 6 HOH B 94 192 192 HOH HOH . O 6 HOH B 95 193 193 HOH HOH . O 6 HOH B 96 194 194 HOH HOH . O 6 HOH B 97 198 198 HOH HOH . O 6 HOH B 98 199 199 HOH HOH . O 6 HOH B 99 200 200 HOH HOH . O 6 HOH B 100 201 201 HOH HOH . O 6 HOH B 101 207 207 HOH HOH . O 6 HOH B 102 209 209 HOH HOH . O 6 HOH B 103 212 212 HOH HOH . O 6 HOH B 104 215 215 HOH HOH . O 6 HOH B 105 218 218 HOH HOH . O 6 HOH B 106 224 224 HOH HOH . O 6 HOH B 107 226 226 HOH HOH . O 6 HOH B 108 229 229 HOH HOH . O 6 HOH B 109 233 233 HOH HOH . O 6 HOH B 110 235 235 HOH HOH . O 6 HOH B 111 237 237 HOH HOH . O 6 HOH B 112 239 239 HOH HOH . O 6 HOH B 113 240 240 HOH HOH . O 6 HOH B 114 241 241 HOH HOH . O 6 HOH B 115 242 242 HOH HOH . O 6 HOH B 116 243 243 HOH HOH . O 6 HOH B 117 244 244 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 PMP . . . C 2 -3.831 43.871 16.715 1 22.29 ? N1 PMP 400 A 1 HETATM 2 C C2 PMP . . . C 2 -3.5 43.383 17.972 1 25.33 ? C2 PMP 400 A 1 HETATM 3 C C2A PMP . . . C 2 -2.508 44.195 18.81 1 21.84 ? C2A PMP 400 A 1 HETATM 4 C C3 PMP . . . C 2 -4.081 42.178 18.404 1 25.93 ? C3 PMP 400 A 1 HETATM 5 O O3 PMP . . . C 2 -3.772 41.666 19.621 1 22.97 ? O3 PMP 400 A 1 HETATM 6 C C4 PMP . . . C 2 -4.998 41.487 17.575 1 23.77 ? C4 PMP 400 A 1 HETATM 7 C C4A PMP . . . C 2 -5.645 40.169 18.094 1 25.42 ? C4A PMP 400 A 1 HETATM 8 N N4A PMP . . . C 2 -4.861 39.099 17.729 1 28.45 ? N4A PMP 400 A 1 HETATM 9 C C5 PMP . . . C 2 -5.294 42.031 16.297 1 27.41 ? C5 PMP 400 A 1 HETATM 10 C C6 PMP . . . C 2 -4.713 43.209 15.883 1 24.55 ? C6 PMP 400 A 1 HETATM 11 C C5A PMP . . . C 2 -6.208 41.354 15.333 1 25.48 ? C5A PMP 400 A 1 HETATM 12 O O4P PMP . . . C 2 -5.658 40.145 14.819 1 24.17 ? O4P PMP 400 A 1 HETATM 13 P P PMP . . . C 2 -6.689 38.989 14.352 1 21.25 ? P PMP 400 A 1 HETATM 14 O O1P PMP . . . C 2 -7.301 38.382 15.525 1 27.57 ? O1P PMP 400 A 1 HETATM 15 O O2P PMP . . . C 2 -5.734 37.977 13.725 1 23.61 ? O2P PMP 400 A 1 HETATM 16 O O3P PMP . . . C 2 -7.572 39.519 13.314 1 25.87 ? O3P PMP 400 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 16 #