data_8B03 # _model_server_result.job_id LlVq1wC3D6AfV6-Y6fXPVg _model_server_result.datetime_utc '2024-11-24 04:29:15' _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 8b03 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8B03 # _exptl.entry_id 8B03 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.67 _cell.angle_gamma 90 _cell.entry_id 8B03 _cell.length_a 182.566 _cell.length_b 60.445 _cell.length_c 67.257 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B03 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 -1 182.566 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 C C4A PLP . B PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? metalc ? metalc1 B O GLY 232 B GLY 232 1_555 D CS CS . B CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc2 B O GLY 268 B GLY 268 1_555 D CS CS . B CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.468 ? metalc ? metalc3 B O PHE 306 B PHE 306 1_555 D CS CS . B CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.032 ? metalc ? metalc4 B O SER 308 B SER 308 1_555 D CS CS . B CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? metalc ? metalc5 D CS CS . B CS 402 1_555 H O HOH . B HOH 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _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 8B03 _atom_sites.fract_transf_matrix[1][1] 0.005477 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000447 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016544 _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] 0.014918 _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 PLP B 1 401 401 PLP PLP . D 4 CS B 1 402 501 CS CS . E 5 CL B 1 403 1 CL CL . F 5 CL B 1 404 2 CL CL . G 6 HOH A 1 301 172 HOH HOH . G 6 HOH A 2 302 73 HOH HOH . G 6 HOH A 3 303 115 HOH HOH . G 6 HOH A 4 304 15 HOH HOH . G 6 HOH A 5 305 215 HOH HOH . G 6 HOH A 6 306 71 HOH HOH . G 6 HOH A 7 307 154 HOH HOH . G 6 HOH A 8 308 89 HOH HOH . G 6 HOH A 9 309 94 HOH HOH . G 6 HOH A 10 310 137 HOH HOH . G 6 HOH A 11 311 177 HOH HOH . G 6 HOH A 12 312 179 HOH HOH . G 6 HOH A 13 313 167 HOH HOH . G 6 HOH A 14 314 91 HOH HOH . G 6 HOH A 15 315 101 HOH HOH . G 6 HOH A 16 316 31 HOH HOH . G 6 HOH A 17 317 65 HOH HOH . G 6 HOH A 18 318 129 HOH HOH . G 6 HOH A 19 319 187 HOH HOH . G 6 HOH A 20 320 27 HOH HOH . G 6 HOH A 21 321 161 HOH HOH . G 6 HOH A 22 322 201 HOH HOH . G 6 HOH A 23 323 152 HOH HOH . G 6 HOH A 24 324 41 HOH HOH . G 6 HOH A 25 325 54 HOH HOH . G 6 HOH A 26 326 85 HOH HOH . G 6 HOH A 27 327 97 HOH HOH . G 6 HOH A 28 328 4 HOH HOH . G 6 HOH A 29 329 75 HOH HOH . G 6 HOH A 30 330 124 HOH HOH . G 6 HOH A 31 331 32 HOH HOH . G 6 HOH A 32 332 51 HOH HOH . G 6 HOH A 33 333 48 HOH HOH . G 6 HOH A 34 334 20 HOH HOH . G 6 HOH A 35 335 11 HOH HOH . G 6 HOH A 36 336 171 HOH HOH . G 6 HOH A 37 337 108 HOH HOH . G 6 HOH A 38 338 13 HOH HOH . G 6 HOH A 39 339 121 HOH HOH . G 6 HOH A 40 340 98 HOH HOH . G 6 HOH A 41 341 88 HOH HOH . G 6 HOH A 42 342 165 HOH HOH . G 6 HOH A 43 343 163 HOH HOH . G 6 HOH A 44 344 224 HOH HOH . G 6 HOH A 45 345 49 HOH HOH . G 6 HOH A 46 346 157 HOH HOH . G 6 HOH A 47 347 211 HOH HOH . G 6 HOH A 48 348 29 HOH HOH . G 6 HOH A 49 349 42 HOH HOH . G 6 HOH A 50 350 223 HOH HOH . G 6 HOH A 51 351 122 HOH HOH . G 6 HOH A 52 352 126 HOH HOH . G 6 HOH A 53 353 105 HOH HOH . G 6 HOH A 54 354 112 HOH HOH . G 6 HOH A 55 355 110 HOH HOH . G 6 HOH A 56 356 214 HOH HOH . G 6 HOH A 57 357 116 HOH HOH . G 6 HOH A 58 358 12 HOH HOH . G 6 HOH A 59 359 33 HOH HOH . G 6 HOH A 60 360 173 HOH HOH . G 6 HOH A 61 361 238 HOH HOH . G 6 HOH A 62 362 220 HOH HOH . G 6 HOH A 63 363 164 HOH HOH . G 6 HOH A 64 364 192 HOH HOH . G 6 HOH A 65 365 190 HOH HOH . G 6 HOH A 66 366 153 HOH HOH . G 6 HOH A 67 367 111 HOH HOH . G 6 HOH A 68 368 236 HOH HOH . G 6 HOH A 69 369 130 HOH HOH . G 6 HOH A 70 370 132 HOH HOH . G 6 HOH A 71 371 178 HOH HOH . G 6 HOH A 72 372 81 HOH HOH . G 6 HOH A 73 373 141 HOH HOH . G 6 HOH A 74 374 213 HOH HOH . G 6 HOH A 75 375 107 HOH HOH . G 6 HOH A 76 376 203 HOH HOH . G 6 HOH A 77 377 204 HOH HOH . G 6 HOH A 78 378 239 HOH HOH . G 6 HOH A 79 379 219 HOH HOH . G 6 HOH A 80 380 62 HOH HOH . G 6 HOH A 81 381 148 HOH HOH . G 6 HOH A 82 382 182 HOH HOH . G 6 HOH A 83 383 208 HOH HOH . G 6 HOH A 84 384 195 HOH HOH . G 6 HOH A 85 385 206 HOH HOH . G 6 HOH A 86 386 114 HOH HOH . H 6 HOH B 1 501 240 HOH HOH . H 6 HOH B 2 502 162 HOH HOH . H 6 HOH B 3 503 70 HOH HOH . H 6 HOH B 4 504 117 HOH HOH . H 6 HOH B 5 505 68 HOH HOH . H 6 HOH B 6 506 87 HOH HOH . H 6 HOH B 7 507 58 HOH HOH . H 6 HOH B 8 508 189 HOH HOH . H 6 HOH B 9 509 228 HOH HOH . H 6 HOH B 10 510 188 HOH HOH . H 6 HOH B 11 511 103 HOH HOH . H 6 HOH B 12 512 84 HOH HOH . H 6 HOH B 13 513 198 HOH HOH . H 6 HOH B 14 514 74 HOH HOH . H 6 HOH B 15 515 53 HOH HOH . H 6 HOH B 16 516 229 HOH HOH . H 6 HOH B 17 517 207 HOH HOH . H 6 HOH B 18 518 176 HOH HOH . H 6 HOH B 19 519 237 HOH HOH . H 6 HOH B 20 520 59 HOH HOH . H 6 HOH B 21 521 184 HOH HOH . H 6 HOH B 22 522 22 HOH HOH . H 6 HOH B 23 523 93 HOH HOH . H 6 HOH B 24 524 72 HOH HOH . H 6 HOH B 25 525 52 HOH HOH . H 6 HOH B 26 526 5 HOH HOH . H 6 HOH B 27 527 202 HOH HOH . H 6 HOH B 28 528 106 HOH HOH . H 6 HOH B 29 529 28 HOH HOH . H 6 HOH B 30 530 21 HOH HOH . H 6 HOH B 31 531 160 HOH HOH . H 6 HOH B 32 532 24 HOH HOH . H 6 HOH B 33 533 6 HOH HOH . H 6 HOH B 34 534 80 HOH HOH . H 6 HOH B 35 535 196 HOH HOH . H 6 HOH B 36 536 61 HOH HOH . H 6 HOH B 37 537 34 HOH HOH . H 6 HOH B 38 538 77 HOH HOH . H 6 HOH B 39 539 35 HOH HOH . H 6 HOH B 40 540 140 HOH HOH . H 6 HOH B 41 541 10 HOH HOH . H 6 HOH B 42 542 40 HOH HOH . H 6 HOH B 43 543 136 HOH HOH . H 6 HOH B 44 544 90 HOH HOH . H 6 HOH B 45 545 43 HOH HOH . H 6 HOH B 46 546 39 HOH HOH . H 6 HOH B 47 547 128 HOH HOH . H 6 HOH B 48 548 232 HOH HOH . H 6 HOH B 49 549 221 HOH HOH . H 6 HOH B 50 550 44 HOH HOH . H 6 HOH B 51 551 241 HOH HOH . H 6 HOH B 52 552 7 HOH HOH . H 6 HOH B 53 553 139 HOH HOH . H 6 HOH B 54 554 66 HOH HOH . H 6 HOH B 55 555 109 HOH HOH . H 6 HOH B 56 556 104 HOH HOH . H 6 HOH B 57 557 69 HOH HOH . H 6 HOH B 58 558 169 HOH HOH . H 6 HOH B 59 559 57 HOH HOH . H 6 HOH B 60 560 30 HOH HOH . H 6 HOH B 61 561 95 HOH HOH . H 6 HOH B 62 562 47 HOH HOH . H 6 HOH B 63 563 225 HOH HOH . H 6 HOH B 64 564 151 HOH HOH . H 6 HOH B 65 565 56 HOH HOH . H 6 HOH B 66 566 18 HOH HOH . H 6 HOH B 67 567 50 HOH HOH . H 6 HOH B 68 568 138 HOH HOH . H 6 HOH B 69 569 37 HOH HOH . H 6 HOH B 70 570 3 HOH HOH . H 6 HOH B 71 571 86 HOH HOH . H 6 HOH B 72 572 134 HOH HOH . H 6 HOH B 73 573 17 HOH HOH . H 6 HOH B 74 574 222 HOH HOH . H 6 HOH B 75 575 181 HOH HOH . H 6 HOH B 76 576 96 HOH HOH . H 6 HOH B 77 577 64 HOH HOH . H 6 HOH B 78 578 14 HOH HOH . H 6 HOH B 79 579 118 HOH HOH . H 6 HOH B 80 580 26 HOH HOH . H 6 HOH B 81 581 25 HOH HOH . H 6 HOH B 82 582 16 HOH HOH . H 6 HOH B 83 583 76 HOH HOH . H 6 HOH B 84 584 23 HOH HOH . H 6 HOH B 85 585 143 HOH HOH . H 6 HOH B 86 586 234 HOH HOH . H 6 HOH B 87 587 127 HOH HOH . H 6 HOH B 88 588 36 HOH HOH . H 6 HOH B 89 589 8 HOH HOH . H 6 HOH B 90 590 113 HOH HOH . H 6 HOH B 91 591 133 HOH HOH . H 6 HOH B 92 592 216 HOH HOH . H 6 HOH B 93 593 166 HOH HOH . H 6 HOH B 94 594 102 HOH HOH . H 6 HOH B 95 595 82 HOH HOH . H 6 HOH B 96 596 200 HOH HOH . H 6 HOH B 97 597 83 HOH HOH . H 6 HOH B 98 598 135 HOH HOH . H 6 HOH B 99 599 227 HOH HOH . H 6 HOH B 100 600 79 HOH HOH . H 6 HOH B 101 601 191 HOH HOH . H 6 HOH B 102 602 120 HOH HOH . H 6 HOH B 103 603 147 HOH HOH . H 6 HOH B 104 604 142 HOH HOH . H 6 HOH B 105 605 2 HOH HOH . H 6 HOH B 106 606 145 HOH HOH . H 6 HOH B 107 607 100 HOH HOH . H 6 HOH B 108 608 149 HOH HOH . H 6 HOH B 109 609 119 HOH HOH . H 6 HOH B 110 610 123 HOH HOH . H 6 HOH B 111 611 159 HOH HOH . H 6 HOH B 112 612 218 HOH HOH . H 6 HOH B 113 613 131 HOH HOH . H 6 HOH B 114 614 19 HOH HOH . H 6 HOH B 115 615 150 HOH HOH . H 6 HOH B 116 616 168 HOH HOH . H 6 HOH B 117 617 55 HOH HOH . H 6 HOH B 118 618 209 HOH HOH . H 6 HOH B 119 619 46 HOH HOH . H 6 HOH B 120 620 38 HOH HOH . H 6 HOH B 121 621 60 HOH HOH . H 6 HOH B 122 622 158 HOH HOH . H 6 HOH B 123 623 9 HOH HOH . H 6 HOH B 124 624 78 HOH HOH . H 6 HOH B 125 625 233 HOH HOH . H 6 HOH B 126 626 235 HOH HOH . H 6 HOH B 127 627 45 HOH HOH . H 6 HOH B 128 628 194 HOH HOH . H 6 HOH B 129 629 199 HOH HOH . H 6 HOH B 130 630 174 HOH HOH . H 6 HOH B 131 631 155 HOH HOH . H 6 HOH B 132 632 180 HOH HOH . H 6 HOH B 133 633 63 HOH HOH . H 6 HOH B 134 634 197 HOH HOH . H 6 HOH B 135 635 125 HOH HOH . H 6 HOH B 136 636 1 HOH HOH . H 6 HOH B 137 637 231 HOH HOH . H 6 HOH B 138 638 212 HOH HOH . H 6 HOH B 139 639 92 HOH HOH . H 6 HOH B 140 640 193 HOH HOH . H 6 HOH B 141 641 185 HOH HOH . H 6 HOH B 142 642 99 HOH HOH . H 6 HOH B 143 643 242 HOH HOH . H 6 HOH B 144 644 186 HOH HOH . H 6 HOH B 145 645 144 HOH HOH . H 6 HOH B 146 646 217 HOH HOH . H 6 HOH B 147 647 210 HOH HOH . H 6 HOH B 148 648 67 HOH HOH . H 6 HOH B 149 649 146 HOH HOH . H 6 HOH B 150 650 183 HOH HOH . H 6 HOH B 151 651 226 HOH HOH . H 6 HOH B 152 652 170 HOH HOH . H 6 HOH B 153 653 230 HOH HOH . H 6 HOH B 154 654 175 HOH HOH . H 6 HOH B 155 655 205 HOH HOH . H 6 HOH B 156 656 156 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 . . . C 3 84.433 13.805 12.003 1 31.84 ? N1 PLP 401 B 1 HETATM 2 C C2 PLP . . . C 3 84.346 14.307 10.722 1 31.67 ? C2 PLP 401 B 1 HETATM 3 C C2A PLP . . . C 3 85.515 14.197 9.791 1 31.06 ? C2A PLP 401 B 1 HETATM 4 C C3 PLP . . . C 3 83.173 14.914 10.295 1 32.52 ? C3 PLP 401 B 1 HETATM 5 O O3 PLP . . . C 3 83.09 15.411 9.022 1 36.1 ? O3 PLP 401 B 1 HETATM 6 C C4 PLP . . . C 3 82.082 15.017 11.153 1 32.61 ? C4 PLP 401 B 1 HETATM 7 C C4A PLP . . . C 3 80.74 15.322 10.55 1 32.45 ? C4A PLP 401 B 1 HETATM 8 C C5 PLP . . . C 3 82.182 14.514 12.45 1 30.78 ? C5 PLP 401 B 1 HETATM 9 C C6 PLP . . . C 3 83.361 13.905 12.863 1 31.88 ? C6 PLP 401 B 1 HETATM 10 C C5A PLP . . . C 3 81.028 14.596 13.427 1 29.8 ? C5A PLP 401 B 1 HETATM 11 O O4P PLP . . . C 3 79.983 13.779 12.956 1 27.1 ? O4P PLP 401 B 1 HETATM 12 P P PLP . . . C 3 79.494 12.508 13.804 1 26.96 ? P PLP 401 B 1 HETATM 13 O O1P PLP . . . C 3 80.325 11.311 13.409 1 26.53 ? O1P PLP 401 B 1 HETATM 14 O O2P PLP . . . C 3 79.67 12.778 15.282 1 28.11 -1 O2P PLP 401 B 1 HETATM 15 O O3P PLP . . . C 3 78.043 12.247 13.492 1 29.1 ? O3P PLP 401 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #