data_8ONJ # _model_server_result.job_id o0gAvcJzL51g6rMPv20Tzw _model_server_result.datetime_utc '2024-11-29 03:50:51' _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 8onj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 8ONJ # _exptl.entry_id 8ONJ _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 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 8ONJ _cell.length_a 60.791 _cell.length_b 88.553 _cell.length_c 100.663 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ONJ _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 D 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 A NZ LYS 144 A LYS 142 1_555 C C4A PLP . A PLP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.27 ? covale ? covale2 B NZ LYS 144 B LYS 142 1_555 D C4A PLP . B PLP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? # _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 276 n y N1 C6 PLP sing 277 n y C2 C2A PLP sing 278 n n C2 C3 PLP sing 279 n y C2A H2A1 PLP sing 280 n n C2A H2A2 PLP sing 281 n n C2A H2A3 PLP sing 282 n n C3 O3 PLP sing 283 n n C3 C4 PLP doub 284 n y O3 HO3 PLP sing 285 n n C4 C4A PLP sing 286 n n C4 C5 PLP sing 287 n y C4A O4A PLP doub 288 n n C4A H4A PLP sing 289 n n C5 C6 PLP doub 290 n y C5 C5A PLP sing 291 n n C6 H6 PLP sing 292 n n C5A O4P PLP sing 293 n n C5A H5A1 PLP sing 294 n n C5A H5A2 PLP sing 295 n n O4P P PLP sing 296 n n P O1P PLP doub 297 n n P O2P PLP sing 298 n n P O3P PLP sing 299 n n O2P HOP2 PLP sing 300 n n O3P HOP3 PLP sing 301 n n # _atom_sites.entry_id 8ONJ _atom_sites.fract_transf_matrix[1][1] 0.01645 _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] 0.011293 _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] 0.009934 _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 PLP A 1 301 301 PLP PLP . D 2 PLP B 1 301 301 PLP PLP . E 3 PEG B 1 302 305 PEG PEG . F 4 HOH A 1 401 247 HOH HOH . F 4 HOH A 2 402 264 HOH HOH . F 4 HOH A 3 403 265 HOH HOH . F 4 HOH A 4 404 198 HOH HOH . F 4 HOH A 5 405 231 HOH HOH . F 4 HOH A 6 406 65 HOH HOH . F 4 HOH A 7 407 130 HOH HOH . F 4 HOH A 8 408 9 HOH HOH . F 4 HOH A 9 409 120 HOH HOH . F 4 HOH A 10 410 85 HOH HOH . F 4 HOH A 11 411 272 HOH HOH . F 4 HOH A 12 412 112 HOH HOH . F 4 HOH A 13 413 229 HOH HOH . F 4 HOH A 14 414 106 HOH HOH . F 4 HOH A 15 415 163 HOH HOH . F 4 HOH A 16 416 201 HOH HOH . F 4 HOH A 17 417 99 HOH HOH . F 4 HOH A 18 418 275 HOH HOH . F 4 HOH A 19 419 91 HOH HOH . F 4 HOH A 20 420 187 HOH HOH . F 4 HOH A 21 421 211 HOH HOH . F 4 HOH A 22 422 102 HOH HOH . F 4 HOH A 23 423 96 HOH HOH . F 4 HOH A 24 424 104 HOH HOH . F 4 HOH A 25 425 93 HOH HOH . F 4 HOH A 26 426 115 HOH HOH . F 4 HOH A 27 427 86 HOH HOH . F 4 HOH A 28 428 81 HOH HOH . F 4 HOH A 29 429 1 HOH HOH . F 4 HOH A 30 430 29 HOH HOH . F 4 HOH A 31 431 268 HOH HOH . F 4 HOH A 32 432 279 HOH HOH . F 4 HOH A 33 433 22 HOH HOH . F 4 HOH A 34 434 255 HOH HOH . F 4 HOH A 35 435 179 HOH HOH . F 4 HOH A 36 436 147 HOH HOH . F 4 HOH A 37 437 23 HOH HOH . F 4 HOH A 38 438 271 HOH HOH . F 4 HOH A 39 439 2 HOH HOH . F 4 HOH A 40 440 230 HOH HOH . F 4 HOH A 41 441 107 HOH HOH . F 4 HOH A 42 442 53 HOH HOH . F 4 HOH A 43 443 31 HOH HOH . F 4 HOH A 44 444 21 HOH HOH . F 4 HOH A 45 445 84 HOH HOH . F 4 HOH A 46 446 83 HOH HOH . F 4 HOH A 47 447 164 HOH HOH . F 4 HOH A 48 448 134 HOH HOH . F 4 HOH A 49 449 6 HOH HOH . F 4 HOH A 50 450 61 HOH HOH . F 4 HOH A 51 451 276 HOH HOH . F 4 HOH A 52 452 254 HOH HOH . F 4 HOH A 53 453 4 HOH HOH . F 4 HOH A 54 454 234 HOH HOH . F 4 HOH A 55 455 20 HOH HOH . F 4 HOH A 56 456 282 HOH HOH . F 4 HOH A 57 457 129 HOH HOH . F 4 HOH A 58 458 35 HOH HOH . F 4 HOH A 59 459 159 HOH HOH . F 4 HOH A 60 460 97 HOH HOH . F 4 HOH A 61 461 213 HOH HOH . F 4 HOH A 62 462 100 HOH HOH . F 4 HOH A 63 463 127 HOH HOH . F 4 HOH A 64 464 148 HOH HOH . F 4 HOH A 65 465 174 HOH HOH . F 4 HOH A 66 466 62 HOH HOH . F 4 HOH A 67 467 277 HOH HOH . F 4 HOH A 68 468 41 HOH HOH . F 4 HOH A 69 469 37 HOH HOH . F 4 HOH A 70 470 46 HOH HOH . F 4 HOH A 71 471 63 HOH HOH . F 4 HOH A 72 472 116 HOH HOH . F 4 HOH A 73 473 253 HOH HOH . F 4 HOH A 74 474 169 HOH HOH . F 4 HOH A 75 475 122 HOH HOH . F 4 HOH A 76 476 10 HOH HOH . F 4 HOH A 77 477 24 HOH HOH . F 4 HOH A 78 478 232 HOH HOH . F 4 HOH A 79 479 17 HOH HOH . F 4 HOH A 80 480 34 HOH HOH . F 4 HOH A 81 481 11 HOH HOH . F 4 HOH A 82 482 70 HOH HOH . F 4 HOH A 83 483 45 HOH HOH . F 4 HOH A 84 484 38 HOH HOH . F 4 HOH A 85 485 150 HOH HOH . F 4 HOH A 86 486 156 HOH HOH . F 4 HOH A 87 487 175 HOH HOH . F 4 HOH A 88 488 108 HOH HOH . F 4 HOH A 89 489 105 HOH HOH . F 4 HOH A 90 490 160 HOH HOH . F 4 HOH A 91 491 36 HOH HOH . F 4 HOH A 92 492 210 HOH HOH . F 4 HOH A 93 493 162 HOH HOH . F 4 HOH A 94 494 26 HOH HOH . F 4 HOH A 95 495 95 HOH HOH . F 4 HOH A 96 496 126 HOH HOH . F 4 HOH A 97 497 145 HOH HOH . F 4 HOH A 98 498 40 HOH HOH . F 4 HOH A 99 499 117 HOH HOH . F 4 HOH A 100 500 49 HOH HOH . F 4 HOH A 101 501 171 HOH HOH . F 4 HOH A 102 502 208 HOH HOH . F 4 HOH A 103 503 82 HOH HOH . F 4 HOH A 104 504 66 HOH HOH . F 4 HOH A 105 505 170 HOH HOH . F 4 HOH A 106 506 109 HOH HOH . F 4 HOH A 107 507 73 HOH HOH . F 4 HOH A 108 508 78 HOH HOH . F 4 HOH A 109 509 52 HOH HOH . F 4 HOH A 110 510 64 HOH HOH . F 4 HOH A 111 511 278 HOH HOH . F 4 HOH A 112 512 79 HOH HOH . F 4 HOH A 113 513 75 HOH HOH . F 4 HOH A 114 514 269 HOH HOH . F 4 HOH A 115 515 228 HOH HOH . F 4 HOH A 116 516 121 HOH HOH . F 4 HOH A 117 517 43 HOH HOH . F 4 HOH A 118 518 136 HOH HOH . F 4 HOH A 119 519 56 HOH HOH . F 4 HOH A 120 520 214 HOH HOH . F 4 HOH A 121 521 205 HOH HOH . F 4 HOH A 122 522 256 HOH HOH . F 4 HOH A 123 523 44 HOH HOH . F 4 HOH A 124 524 209 HOH HOH . F 4 HOH A 125 525 183 HOH HOH . F 4 HOH A 126 526 103 HOH HOH . F 4 HOH A 127 527 259 HOH HOH . F 4 HOH A 128 528 30 HOH HOH . F 4 HOH A 129 529 153 HOH HOH . F 4 HOH A 130 530 220 HOH HOH . F 4 HOH A 131 531 263 HOH HOH . F 4 HOH A 132 532 154 HOH HOH . F 4 HOH A 133 533 215 HOH HOH . F 4 HOH A 134 534 184 HOH HOH . F 4 HOH A 135 535 177 HOH HOH . F 4 HOH A 136 536 199 HOH HOH . F 4 HOH A 137 537 202 HOH HOH . F 4 HOH A 138 538 189 HOH HOH . F 4 HOH A 139 539 118 HOH HOH . F 4 HOH A 140 540 245 HOH HOH . F 4 HOH A 141 541 233 HOH HOH . F 4 HOH A 142 542 217 HOH HOH . F 4 HOH A 143 543 207 HOH HOH . F 4 HOH A 144 544 165 HOH HOH . F 4 HOH A 145 545 135 HOH HOH . F 4 HOH A 146 546 178 HOH HOH . F 4 HOH A 147 547 224 HOH HOH . F 4 HOH A 148 548 146 HOH HOH . F 4 HOH A 149 549 191 HOH HOH . F 4 HOH A 150 550 101 HOH HOH . F 4 HOH A 151 551 235 HOH HOH . G 4 HOH B 1 401 258 HOH HOH . G 4 HOH B 2 402 7 HOH HOH . G 4 HOH B 3 403 151 HOH HOH . G 4 HOH B 4 404 223 HOH HOH . G 4 HOH B 5 405 88 HOH HOH . G 4 HOH B 6 406 181 HOH HOH . G 4 HOH B 7 407 274 HOH HOH . G 4 HOH B 8 408 280 HOH HOH . G 4 HOH B 9 409 8 HOH HOH . G 4 HOH B 10 410 12 HOH HOH . G 4 HOH B 11 411 142 HOH HOH . G 4 HOH B 12 412 144 HOH HOH . G 4 HOH B 13 413 196 HOH HOH . G 4 HOH B 14 414 172 HOH HOH . G 4 HOH B 15 415 283 HOH HOH . G 4 HOH B 16 416 27 HOH HOH . G 4 HOH B 17 417 242 HOH HOH . G 4 HOH B 18 418 60 HOH HOH . G 4 HOH B 19 419 113 HOH HOH . G 4 HOH B 20 420 16 HOH HOH . G 4 HOH B 21 421 110 HOH HOH . G 4 HOH B 22 422 58 HOH HOH . G 4 HOH B 23 423 13 HOH HOH . G 4 HOH B 24 424 281 HOH HOH . G 4 HOH B 25 425 257 HOH HOH . G 4 HOH B 26 426 51 HOH HOH . G 4 HOH B 27 427 15 HOH HOH . G 4 HOH B 28 428 39 HOH HOH . G 4 HOH B 29 429 123 HOH HOH . G 4 HOH B 30 430 87 HOH HOH . G 4 HOH B 31 431 19 HOH HOH . G 4 HOH B 32 432 212 HOH HOH . G 4 HOH B 33 433 206 HOH HOH . G 4 HOH B 34 434 28 HOH HOH . G 4 HOH B 35 435 32 HOH HOH . G 4 HOH B 36 436 124 HOH HOH . G 4 HOH B 37 437 138 HOH HOH . G 4 HOH B 38 438 25 HOH HOH . G 4 HOH B 39 439 76 HOH HOH . G 4 HOH B 40 440 47 HOH HOH . G 4 HOH B 41 441 185 HOH HOH . G 4 HOH B 42 442 42 HOH HOH . G 4 HOH B 43 443 89 HOH HOH . G 4 HOH B 44 444 59 HOH HOH . G 4 HOH B 45 445 192 HOH HOH . G 4 HOH B 46 446 193 HOH HOH . G 4 HOH B 47 447 77 HOH HOH . G 4 HOH B 48 448 57 HOH HOH . G 4 HOH B 49 449 243 HOH HOH . G 4 HOH B 50 450 186 HOH HOH . G 4 HOH B 51 451 111 HOH HOH . G 4 HOH B 52 452 140 HOH HOH . G 4 HOH B 53 453 119 HOH HOH . G 4 HOH B 54 454 67 HOH HOH . G 4 HOH B 55 455 114 HOH HOH . G 4 HOH B 56 456 143 HOH HOH . G 4 HOH B 57 457 128 HOH HOH . G 4 HOH B 58 458 131 HOH HOH . G 4 HOH B 59 459 68 HOH HOH . G 4 HOH B 60 460 92 HOH HOH . G 4 HOH B 61 461 270 HOH HOH . G 4 HOH B 62 462 3 HOH HOH . G 4 HOH B 63 463 240 HOH HOH . G 4 HOH B 64 464 239 HOH HOH . G 4 HOH B 65 465 48 HOH HOH . G 4 HOH B 66 466 141 HOH HOH . G 4 HOH B 67 467 98 HOH HOH . G 4 HOH B 68 468 226 HOH HOH . G 4 HOH B 69 469 72 HOH HOH . G 4 HOH B 70 470 161 HOH HOH . G 4 HOH B 71 471 200 HOH HOH . G 4 HOH B 72 472 137 HOH HOH . G 4 HOH B 73 473 216 HOH HOH . G 4 HOH B 74 474 158 HOH HOH . G 4 HOH B 75 475 237 HOH HOH . G 4 HOH B 76 476 167 HOH HOH . G 4 HOH B 77 477 173 HOH HOH . G 4 HOH B 78 478 225 HOH HOH . G 4 HOH B 79 479 74 HOH HOH . G 4 HOH B 80 480 69 HOH HOH . G 4 HOH B 81 481 260 HOH HOH . G 4 HOH B 82 482 180 HOH HOH . G 4 HOH B 83 483 197 HOH HOH . G 4 HOH B 84 484 33 HOH HOH . G 4 HOH B 85 485 55 HOH HOH . G 4 HOH B 86 486 71 HOH HOH . G 4 HOH B 87 487 222 HOH HOH . G 4 HOH B 88 488 188 HOH HOH . G 4 HOH B 89 489 168 HOH HOH . G 4 HOH B 90 490 133 HOH HOH . G 4 HOH B 91 491 50 HOH HOH . G 4 HOH B 92 492 190 HOH HOH . G 4 HOH B 93 493 241 HOH HOH . G 4 HOH B 94 494 262 HOH HOH . G 4 HOH B 95 495 267 HOH HOH . G 4 HOH B 96 496 236 HOH HOH . G 4 HOH B 97 497 152 HOH HOH . G 4 HOH B 98 498 273 HOH HOH . G 4 HOH B 99 499 227 HOH HOH . G 4 HOH B 100 500 244 HOH HOH . G 4 HOH B 101 501 132 HOH HOH . G 4 HOH B 102 502 90 HOH HOH . G 4 HOH B 103 503 238 HOH HOH . G 4 HOH B 104 504 194 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 . . . D 2 -14.141 -7.21 -22.709 1 20.45 ? N1 PLP 301 B 1 HETATM 2 C C2 PLP . . . D 2 -14.974 -6.197 -22.426 1 21.58 ? C2 PLP 301 B 1 HETATM 3 C C2A PLP . . . D 2 -15.903 -6.316 -21.259 1 24.7 ? C2A PLP 301 B 1 HETATM 4 C C3 PLP . . . D 2 -15.056 -5.091 -23.264 1 21.54 ? C3 PLP 301 B 1 HETATM 5 O O3 PLP . . . D 2 -15.947 -4.105 -22.974 1 21.67 ? O3 PLP 301 B 1 HETATM 6 C C4 PLP . . . D 2 -14.222 -5.029 -24.401 1 21.29 ? C4 PLP 301 B 1 HETATM 7 C C4A PLP . . . D 2 -14.357 -3.86 -25.266 1 22.48 ? C4A PLP 301 B 1 HETATM 8 C C5 PLP . . . D 2 -13.25 -6.056 -24.593 1 20.45 ? C5 PLP 301 B 1 HETATM 9 C C6 PLP . . . D 2 -13.306 -7.147 -23.761 1 19.39 ? C6 PLP 301 B 1 HETATM 10 C C5A PLP . . . D 2 -12.304 -6.07 -25.769 1 19.4 ? C5A PLP 301 B 1 HETATM 11 O O4P PLP . . . D 2 -12.958 -6.358 -27.042 1 18.89 ? O4P PLP 301 B 1 HETATM 12 P P PLP . . . D 2 -11.997 -6.162 -28.337 1 21.19 ? P PLP 301 B 1 HETATM 13 O O1P PLP . . . D 2 -13.075 -6.4 -29.396 1 19.97 ? O1P PLP 301 B 1 HETATM 14 O O2P PLP . . . D 2 -11.417 -4.714 -28.329 1 22.88 ? O2P PLP 301 B 1 HETATM 15 O O3P PLP . . . D 2 -10.874 -7.219 -28.203 1 17.87 ? O3P PLP 301 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #