data_1WDW # _model_server_result.job_id BbE8-YT1wGwuAZsQMo7f5g _model_server_result.datetime_utc '2024-12-22 05:56:57' _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 1wdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":400}' # _entry.id 1WDW # _exptl.entry_id 1WDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 1WDW _cell.length_a 89.056 _cell.length_b 220.257 _cell.length_c 292.56 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA tetrameric 4 author_and_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,B,C,D,M,N,S,T,U 1 1 E,F,G,H,O,P,V,W,X,Y 2 1 I,J,K,L,Q,R,Z,AA,BA 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 ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R 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 covale ? covale1 B NZ LYS 82 B LYS 82 1_555 M C4A PLP . B PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale2 D NZ LYS 82 D LYS 82 1_555 N C4A PLP . D PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale3 F NZ LYS 82 F LYS 82 1_555 O C4A PLP . F PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale4 H NZ LYS 82 H LYS 82 1_555 P C4A PLP . H PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale5 J NZ LYS 82 J LYS 82 1_555 Q C4A PLP . J PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale6 L NZ LYS 82 L LYS 82 1_555 R C4A PLP . L PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? # _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 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 1WDW _atom_sites.fract_transf_matrix[1][1] 0.011229 _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] 0.00454 _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] 0.003418 _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 M 3 PLP B 1 400 400 PLP PLP . N 3 PLP D 1 400 400 PLP PLP . O 3 PLP F 1 400 400 PLP PLP . P 3 PLP H 1 400 400 PLP PLP . Q 3 PLP J 1 400 400 PLP PLP . R 3 PLP L 1 400 400 PLP PLP . S 4 HOH B 1 401 1 HOH HOH . S 4 HOH B 2 402 8 HOH HOH . S 4 HOH B 3 403 10 HOH HOH . S 4 HOH B 4 404 12 HOH HOH . S 4 HOH B 5 405 14 HOH HOH . S 4 HOH B 6 406 16 HOH HOH . S 4 HOH B 7 407 19 HOH HOH . S 4 HOH B 8 408 23 HOH HOH . S 4 HOH B 9 409 28 HOH HOH . S 4 HOH B 10 410 31 HOH HOH . S 4 HOH B 11 411 34 HOH HOH . S 4 HOH B 12 412 38 HOH HOH . S 4 HOH B 13 413 41 HOH HOH . S 4 HOH B 14 414 45 HOH HOH . S 4 HOH B 15 415 283 HOH HOH . S 4 HOH B 16 416 284 HOH HOH . S 4 HOH B 17 417 285 HOH HOH . S 4 HOH B 18 418 286 HOH HOH . S 4 HOH B 19 419 287 HOH HOH . S 4 HOH B 20 420 306 HOH HOH . S 4 HOH B 21 421 316 HOH HOH . S 4 HOH B 22 422 317 HOH HOH . S 4 HOH B 23 423 318 HOH HOH . T 4 HOH C 1 249 7 HOH HOH . T 4 HOH C 2 250 44 HOH HOH . U 4 HOH D 1 401 2 HOH HOH . U 4 HOH D 2 402 11 HOH HOH . U 4 HOH D 3 403 27 HOH HOH . U 4 HOH D 4 404 29 HOH HOH . U 4 HOH D 5 405 30 HOH HOH . U 4 HOH D 6 406 35 HOH HOH . U 4 HOH D 7 407 39 HOH HOH . U 4 HOH D 8 408 40 HOH HOH . U 4 HOH D 9 409 42 HOH HOH . U 4 HOH D 10 410 66 HOH HOH . U 4 HOH D 11 411 73 HOH HOH . U 4 HOH D 12 412 74 HOH HOH . U 4 HOH D 13 413 79 HOH HOH . U 4 HOH D 14 414 91 HOH HOH . U 4 HOH D 15 415 92 HOH HOH . U 4 HOH D 16 416 93 HOH HOH . U 4 HOH D 17 417 290 HOH HOH . U 4 HOH D 18 418 291 HOH HOH . U 4 HOH D 19 419 292 HOH HOH . U 4 HOH D 20 420 293 HOH HOH . U 4 HOH D 21 421 294 HOH HOH . U 4 HOH D 22 422 308 HOH HOH . U 4 HOH D 23 423 313 HOH HOH . V 4 HOH E 1 249 67 HOH HOH . V 4 HOH E 2 250 95 HOH HOH . V 4 HOH E 3 251 100 HOH HOH . V 4 HOH E 4 252 114 HOH HOH . W 4 HOH F 1 401 3 HOH HOH . W 4 HOH F 2 402 48 HOH HOH . W 4 HOH F 3 403 52 HOH HOH . W 4 HOH F 4 404 53 HOH HOH . W 4 HOH F 5 405 55 HOH HOH . W 4 HOH F 6 406 61 HOH HOH . W 4 HOH F 7 407 62 HOH HOH . W 4 HOH F 8 408 63 HOH HOH . W 4 HOH F 9 409 65 HOH HOH . W 4 HOH F 10 410 112 HOH HOH . W 4 HOH F 11 411 113 HOH HOH . W 4 HOH F 12 412 116 HOH HOH . W 4 HOH F 13 413 117 HOH HOH . W 4 HOH F 14 414 118 HOH HOH . W 4 HOH F 15 415 119 HOH HOH . W 4 HOH F 16 416 126 HOH HOH . W 4 HOH F 17 417 127 HOH HOH . W 4 HOH F 18 418 135 HOH HOH . W 4 HOH F 19 419 136 HOH HOH . W 4 HOH F 20 420 137 HOH HOH . W 4 HOH F 21 421 138 HOH HOH . W 4 HOH F 22 422 139 HOH HOH . W 4 HOH F 23 423 140 HOH HOH . W 4 HOH F 24 424 141 HOH HOH . W 4 HOH F 25 425 296 HOH HOH . W 4 HOH F 26 426 297 HOH HOH . W 4 HOH F 27 427 298 HOH HOH . W 4 HOH F 28 428 299 HOH HOH . W 4 HOH F 29 429 300 HOH HOH . W 4 HOH F 30 430 303 HOH HOH . W 4 HOH F 31 431 312 HOH HOH . W 4 HOH F 32 432 314 HOH HOH . W 4 HOH F 33 433 315 HOH HOH . X 4 HOH G 1 249 13 HOH HOH . X 4 HOH G 2 250 143 HOH HOH . X 4 HOH G 3 251 146 HOH HOH . X 4 HOH G 4 252 148 HOH HOH . X 4 HOH G 5 253 149 HOH HOH . X 4 HOH G 6 254 150 HOH HOH . X 4 HOH G 7 255 152 HOH HOH . X 4 HOH G 8 256 302 HOH HOH . X 4 HOH G 9 257 305 HOH HOH . Y 4 HOH H 1 401 4 HOH HOH . Y 4 HOH H 2 402 15 HOH HOH . Y 4 HOH H 3 403 59 HOH HOH . Y 4 HOH H 4 404 75 HOH HOH . Y 4 HOH H 5 405 76 HOH HOH . Y 4 HOH H 6 406 77 HOH HOH . Y 4 HOH H 7 407 78 HOH HOH . Y 4 HOH H 8 408 81 HOH HOH . Y 4 HOH H 9 409 83 HOH HOH . Y 4 HOH H 10 410 85 HOH HOH . Y 4 HOH H 11 411 86 HOH HOH . Y 4 HOH H 12 412 87 HOH HOH . Y 4 HOH H 13 413 89 HOH HOH . Y 4 HOH H 14 414 153 HOH HOH . Y 4 HOH H 15 415 154 HOH HOH . Y 4 HOH H 16 416 157 HOH HOH . Y 4 HOH H 17 417 160 HOH HOH . Y 4 HOH H 18 418 161 HOH HOH . Y 4 HOH H 19 419 163 HOH HOH . Y 4 HOH H 20 420 166 HOH HOH . Y 4 HOH H 21 421 167 HOH HOH . Y 4 HOH H 22 422 168 HOH HOH . Y 4 HOH H 23 423 169 HOH HOH . Y 4 HOH H 24 424 170 HOH HOH . Y 4 HOH H 25 425 172 HOH HOH . Y 4 HOH H 26 426 173 HOH HOH . Y 4 HOH H 27 427 177 HOH HOH . Y 4 HOH H 28 428 178 HOH HOH . Y 4 HOH H 29 429 179 HOH HOH . Y 4 HOH H 30 430 180 HOH HOH . Y 4 HOH H 31 431 183 HOH HOH . Y 4 HOH H 32 432 184 HOH HOH . Y 4 HOH H 33 433 185 HOH HOH . Y 4 HOH H 34 434 186 HOH HOH . Y 4 HOH H 35 435 187 HOH HOH . Y 4 HOH H 36 436 304 HOH HOH . Z 4 HOH I 1 249 20 HOH HOH . Z 4 HOH I 2 250 22 HOH HOH . Z 4 HOH I 3 251 189 HOH HOH . Z 4 HOH I 4 252 190 HOH HOH . Z 4 HOH I 5 253 193 HOH HOH . Z 4 HOH I 6 254 194 HOH HOH . Z 4 HOH I 7 255 195 HOH HOH . Z 4 HOH I 8 256 196 HOH HOH . Z 4 HOH I 9 257 198 HOH HOH . Z 4 HOH I 10 258 199 HOH HOH . Z 4 HOH I 11 259 200 HOH HOH . Z 4 HOH I 12 260 205 HOH HOH . Z 4 HOH I 13 261 288 HOH HOH . AA 4 HOH J 1 401 5 HOH HOH . AA 4 HOH J 2 402 18 HOH HOH . AA 4 HOH J 3 403 96 HOH HOH . AA 4 HOH J 4 404 97 HOH HOH . AA 4 HOH J 5 405 98 HOH HOH . AA 4 HOH J 6 406 99 HOH HOH . AA 4 HOH J 7 407 101 HOH HOH . AA 4 HOH J 8 408 102 HOH HOH . AA 4 HOH J 9 409 106 HOH HOH . AA 4 HOH J 10 410 107 HOH HOH . AA 4 HOH J 11 411 108 HOH HOH . AA 4 HOH J 12 412 109 HOH HOH . AA 4 HOH J 13 413 110 HOH HOH . AA 4 HOH J 14 414 111 HOH HOH . AA 4 HOH J 15 415 115 HOH HOH . AA 4 HOH J 16 416 128 HOH HOH . AA 4 HOH J 17 417 201 HOH HOH . AA 4 HOH J 18 418 202 HOH HOH . AA 4 HOH J 19 419 203 HOH HOH . AA 4 HOH J 20 420 204 HOH HOH . AA 4 HOH J 21 421 206 HOH HOH . AA 4 HOH J 22 422 207 HOH HOH . AA 4 HOH J 23 423 208 HOH HOH . AA 4 HOH J 24 424 210 HOH HOH . AA 4 HOH J 25 425 211 HOH HOH . AA 4 HOH J 26 426 212 HOH HOH . AA 4 HOH J 27 427 213 HOH HOH . AA 4 HOH J 28 428 214 HOH HOH . AA 4 HOH J 29 429 217 HOH HOH . AA 4 HOH J 30 430 218 HOH HOH . AA 4 HOH J 31 431 220 HOH HOH . AA 4 HOH J 32 432 221 HOH HOH . AA 4 HOH J 33 433 222 HOH HOH . AA 4 HOH J 34 434 223 HOH HOH . AA 4 HOH J 35 435 226 HOH HOH . AA 4 HOH J 36 436 227 HOH HOH . AA 4 HOH J 37 437 228 HOH HOH . AA 4 HOH J 38 438 229 HOH HOH . AA 4 HOH J 39 439 232 HOH HOH . AA 4 HOH J 40 440 233 HOH HOH . AA 4 HOH J 41 441 235 HOH HOH . AA 4 HOH J 42 442 261 HOH HOH . AA 4 HOH J 43 443 311 HOH HOH . BA 4 HOH L 1 401 103 HOH HOH . BA 4 HOH L 2 402 104 HOH HOH . BA 4 HOH L 3 403 120 HOH HOH . BA 4 HOH L 4 404 121 HOH HOH . BA 4 HOH L 5 405 122 HOH HOH . BA 4 HOH L 6 406 123 HOH HOH . BA 4 HOH L 7 407 124 HOH HOH . BA 4 HOH L 8 408 125 HOH HOH . BA 4 HOH L 9 409 129 HOH HOH . BA 4 HOH L 10 410 130 HOH HOH . BA 4 HOH L 11 411 131 HOH HOH . BA 4 HOH L 12 412 132 HOH HOH . BA 4 HOH L 13 413 133 HOH HOH . BA 4 HOH L 14 414 134 HOH HOH . BA 4 HOH L 15 415 250 HOH HOH . BA 4 HOH L 16 416 251 HOH HOH . BA 4 HOH L 17 417 253 HOH HOH . BA 4 HOH L 18 418 254 HOH HOH . BA 4 HOH L 19 419 255 HOH HOH . BA 4 HOH L 20 420 260 HOH HOH . BA 4 HOH L 21 421 262 HOH HOH . BA 4 HOH L 22 422 263 HOH HOH . BA 4 HOH L 23 423 264 HOH HOH . BA 4 HOH L 24 424 265 HOH HOH . BA 4 HOH L 25 425 266 HOH HOH . BA 4 HOH L 26 426 268 HOH HOH . BA 4 HOH L 27 427 270 HOH HOH . BA 4 HOH L 28 428 272 HOH HOH . BA 4 HOH L 29 429 273 HOH HOH . BA 4 HOH L 30 430 274 HOH HOH . BA 4 HOH L 31 431 276 HOH HOH . BA 4 HOH L 32 432 277 HOH HOH . BA 4 HOH L 33 433 279 HOH HOH . BA 4 HOH L 34 434 280 HOH HOH . BA 4 HOH L 35 435 310 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 . . . M 3 85.813 215.371 172.305 1 83.27 ? N1 PLP 400 B 1 HETATM 2 C C2 PLP . . . M 3 85.098 215.681 171.162 1 78.01 ? C2 PLP 400 B 1 HETATM 3 C C2A PLP . . . M 3 85.207 214.673 170.025 1 88.97 ? C2A PLP 400 B 1 HETATM 4 C C3 PLP . . . M 3 84.334 216.841 171.148 1 78.79 ? C3 PLP 400 B 1 HETATM 5 O O3 PLP . . . M 3 83.65 217.085 169.987 1 91.95 ? O3 PLP 400 B 1 HETATM 6 C C4 PLP . . . M 3 84.283 217.734 172.225 1 69.34 ? C4 PLP 400 B 1 HETATM 7 C C4A PLP . . . M 3 83.42 219.017 172.154 1 77.09 ? C4A PLP 400 B 1 HETATM 8 C C5 PLP . . . M 3 85.023 217.419 173.414 1 74.3 ? C5 PLP 400 B 1 HETATM 9 C C6 PLP . . . M 3 85.768 216.239 173.378 1 85.26 ? C6 PLP 400 B 1 HETATM 10 C C5A PLP . . . M 3 85.124 218.238 174.706 1 62.46 ? C5A PLP 400 B 1 HETATM 11 O O4P PLP . . . M 3 83.97 218.443 175.494 1 55.9 ? O4P PLP 400 B 1 HETATM 12 P P PLP . . . M 3 83.671 217.593 176.776 1 68.71 ? P PLP 400 B 1 HETATM 13 O O1P PLP . . . M 3 82.405 218.202 177.235 1 55.57 ? O1P PLP 400 B 1 HETATM 14 O O2P PLP . . . M 3 84.809 217.819 177.711 1 63.55 ? O2P PLP 400 B 1 HETATM 15 O O3P PLP . . . M 3 83.49 216.187 176.464 1 63.41 ? O3P PLP 400 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #