data_1K7E # _model_server_result.job_id SiiUfDnkfK8J5iWhIMIMOA _model_server_result.datetime_utc '2024-12-21 16:18:06' _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 1k7e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 1K7E # _exptl.entry_id 1K7E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _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 94.55 _cell.angle_gamma 90 _cell.entry_id 1K7E _cell.length_a 182.651 _cell.length_b 59.081 _cell.length_c 67.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K7E _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 -1 182.651 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 86 B LYS 87 1_555 E C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? metalc ? metalc1 B O GLY 231 B GLY 232 1_555 D NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 B O PHE 305 B PHE 306 1_555 D NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc3 B O SER 307 B SER 308 1_555 D NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 D NA NA . B NA 403 1_555 G O HOH . B HOH 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc5 D NA NA . B NA 403 1_555 G O HOH . B HOH 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? # _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 290 n y N1 C6 PLP sing 291 n y C2 C2A PLP sing 292 n n C2 C3 PLP sing 293 n y C2A H2A1 PLP sing 294 n n C2A H2A2 PLP sing 295 n n C2A H2A3 PLP sing 296 n n C3 O3 PLP sing 297 n n C3 C4 PLP doub 298 n y O3 HO3 PLP sing 299 n n C4 C4A PLP sing 300 n n C4 C5 PLP sing 301 n y C4A O4A PLP doub 302 n n C4A H4A PLP sing 303 n n C5 C6 PLP doub 304 n y C5 C5A PLP sing 305 n n C6 H6 PLP sing 306 n n C5A O4P PLP sing 307 n n C5A H5A1 PLP sing 308 n n C5A H5A2 PLP sing 309 n n O4P P PLP sing 310 n n P O1P PLP doub 311 n n P O2P PLP sing 312 n n P O3P PLP sing 313 n n O2P HOP2 PLP sing 314 n n O3P HOP3 PLP sing 315 n n # _atom_sites.entry_id 1K7E _atom_sites.fract_transf_matrix[1][1] 0.005475 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000436 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016926 _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] 0.014906 _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 IAG A 1 401 1 IAG IAG . D 4 NA B 1 403 3 NA NA . E 5 PLP B 1 402 2 PLP PLP . F 6 HOH A 1 402 6 HOH HOH . F 6 HOH A 2 403 7 HOH HOH . F 6 HOH A 3 404 9 HOH HOH . F 6 HOH A 4 405 11 HOH HOH . F 6 HOH A 5 406 12 HOH HOH . F 6 HOH A 6 407 16 HOH HOH . F 6 HOH A 7 408 17 HOH HOH . F 6 HOH A 8 409 18 HOH HOH . F 6 HOH A 9 410 24 HOH HOH . F 6 HOH A 10 411 29 HOH HOH . F 6 HOH A 11 412 36 HOH HOH . F 6 HOH A 12 413 37 HOH HOH . F 6 HOH A 13 414 38 HOH HOH . F 6 HOH A 14 415 40 HOH HOH . F 6 HOH A 15 416 42 HOH HOH . F 6 HOH A 16 417 44 HOH HOH . F 6 HOH A 17 418 53 HOH HOH . F 6 HOH A 18 419 58 HOH HOH . F 6 HOH A 19 420 59 HOH HOH . F 6 HOH A 20 421 60 HOH HOH . F 6 HOH A 21 422 61 HOH HOH . F 6 HOH A 22 423 65 HOH HOH . F 6 HOH A 23 424 66 HOH HOH . F 6 HOH A 24 425 69 HOH HOH . F 6 HOH A 25 426 70 HOH HOH . F 6 HOH A 26 427 71 HOH HOH . F 6 HOH A 27 428 72 HOH HOH . F 6 HOH A 28 429 78 HOH HOH . F 6 HOH A 29 430 80 HOH HOH . F 6 HOH A 30 431 82 HOH HOH . F 6 HOH A 31 432 83 HOH HOH . F 6 HOH A 32 433 84 HOH HOH . F 6 HOH A 33 434 85 HOH HOH . F 6 HOH A 34 435 87 HOH HOH . F 6 HOH A 35 436 88 HOH HOH . F 6 HOH A 36 437 89 HOH HOH . F 6 HOH A 37 438 103 HOH HOH . F 6 HOH A 38 439 104 HOH HOH . F 6 HOH A 39 440 110 HOH HOH . F 6 HOH A 40 441 114 HOH HOH . F 6 HOH A 41 442 116 HOH HOH . F 6 HOH A 42 443 121 HOH HOH . F 6 HOH A 43 444 123 HOH HOH . F 6 HOH A 44 445 124 HOH HOH . F 6 HOH A 45 446 125 HOH HOH . F 6 HOH A 46 447 126 HOH HOH . F 6 HOH A 47 448 128 HOH HOH . F 6 HOH A 48 449 130 HOH HOH . F 6 HOH A 49 450 131 HOH HOH . F 6 HOH A 50 451 132 HOH HOH . F 6 HOH A 51 452 137 HOH HOH . F 6 HOH A 52 453 139 HOH HOH . F 6 HOH A 53 454 141 HOH HOH . F 6 HOH A 54 455 145 HOH HOH . F 6 HOH A 55 456 148 HOH HOH . F 6 HOH A 56 457 149 HOH HOH . F 6 HOH A 57 458 155 HOH HOH . F 6 HOH A 58 459 156 HOH HOH . F 6 HOH A 59 460 157 HOH HOH . F 6 HOH A 60 461 159 HOH HOH . F 6 HOH A 61 462 163 HOH HOH . F 6 HOH A 62 463 167 HOH HOH . F 6 HOH A 63 464 169 HOH HOH . F 6 HOH A 64 465 171 HOH HOH . F 6 HOH A 65 466 172 HOH HOH . F 6 HOH A 66 467 173 HOH HOH . F 6 HOH A 67 468 176 HOH HOH . F 6 HOH A 68 469 178 HOH HOH . F 6 HOH A 69 470 184 HOH HOH . F 6 HOH A 70 471 194 HOH HOH . F 6 HOH A 71 472 206 HOH HOH . F 6 HOH A 72 473 213 HOH HOH . F 6 HOH A 73 474 216 HOH HOH . F 6 HOH A 74 475 217 HOH HOH . F 6 HOH A 75 476 218 HOH HOH . F 6 HOH A 76 477 219 HOH HOH . F 6 HOH A 77 478 222 HOH HOH . F 6 HOH A 78 479 224 HOH HOH . F 6 HOH A 79 480 225 HOH HOH . F 6 HOH A 80 481 227 HOH HOH . F 6 HOH A 81 482 231 HOH HOH . F 6 HOH A 82 483 236 HOH HOH . G 6 HOH B 1 404 1 HOH HOH . G 6 HOH B 2 405 2 HOH HOH . G 6 HOH B 3 406 3 HOH HOH . G 6 HOH B 4 407 4 HOH HOH . G 6 HOH B 5 408 5 HOH HOH . G 6 HOH B 6 409 8 HOH HOH . G 6 HOH B 7 410 10 HOH HOH . G 6 HOH B 8 411 13 HOH HOH . G 6 HOH B 9 412 14 HOH HOH . G 6 HOH B 10 413 15 HOH HOH . G 6 HOH B 11 414 19 HOH HOH . G 6 HOH B 12 415 20 HOH HOH . G 6 HOH B 13 416 21 HOH HOH . G 6 HOH B 14 417 22 HOH HOH . G 6 HOH B 15 418 23 HOH HOH . G 6 HOH B 16 419 25 HOH HOH . G 6 HOH B 17 420 26 HOH HOH . G 6 HOH B 18 421 27 HOH HOH . G 6 HOH B 19 422 28 HOH HOH . G 6 HOH B 20 423 30 HOH HOH . G 6 HOH B 21 424 31 HOH HOH . G 6 HOH B 22 425 32 HOH HOH . G 6 HOH B 23 426 33 HOH HOH . G 6 HOH B 24 427 34 HOH HOH . G 6 HOH B 25 428 35 HOH HOH . G 6 HOH B 26 429 39 HOH HOH . G 6 HOH B 27 430 41 HOH HOH . G 6 HOH B 28 431 43 HOH HOH . G 6 HOH B 29 432 45 HOH HOH . G 6 HOH B 30 433 46 HOH HOH . G 6 HOH B 31 434 47 HOH HOH . G 6 HOH B 32 435 48 HOH HOH . G 6 HOH B 33 436 49 HOH HOH . G 6 HOH B 34 437 50 HOH HOH . G 6 HOH B 35 438 51 HOH HOH . G 6 HOH B 36 439 52 HOH HOH . G 6 HOH B 37 440 54 HOH HOH . G 6 HOH B 38 441 55 HOH HOH . G 6 HOH B 39 442 56 HOH HOH . G 6 HOH B 40 443 57 HOH HOH . G 6 HOH B 41 444 62 HOH HOH . G 6 HOH B 42 445 63 HOH HOH . G 6 HOH B 43 446 64 HOH HOH . G 6 HOH B 44 447 67 HOH HOH . G 6 HOH B 45 448 68 HOH HOH . G 6 HOH B 46 449 73 HOH HOH . G 6 HOH B 47 450 74 HOH HOH . G 6 HOH B 48 451 75 HOH HOH . G 6 HOH B 49 452 76 HOH HOH . G 6 HOH B 50 453 77 HOH HOH . G 6 HOH B 51 454 79 HOH HOH . G 6 HOH B 52 455 81 HOH HOH . G 6 HOH B 53 456 86 HOH HOH . G 6 HOH B 54 457 90 HOH HOH . G 6 HOH B 55 458 91 HOH HOH . G 6 HOH B 56 459 92 HOH HOH . G 6 HOH B 57 460 93 HOH HOH . G 6 HOH B 58 461 94 HOH HOH . G 6 HOH B 59 462 95 HOH HOH . G 6 HOH B 60 463 96 HOH HOH . G 6 HOH B 61 464 97 HOH HOH . G 6 HOH B 62 465 98 HOH HOH . G 6 HOH B 63 466 99 HOH HOH . G 6 HOH B 64 467 100 HOH HOH . G 6 HOH B 65 468 101 HOH HOH . G 6 HOH B 66 469 102 HOH HOH . G 6 HOH B 67 470 105 HOH HOH . G 6 HOH B 68 471 106 HOH HOH . G 6 HOH B 69 472 107 HOH HOH . G 6 HOH B 70 473 108 HOH HOH . G 6 HOH B 71 474 109 HOH HOH . G 6 HOH B 72 475 111 HOH HOH . G 6 HOH B 73 476 112 HOH HOH . G 6 HOH B 74 477 113 HOH HOH . G 6 HOH B 75 478 115 HOH HOH . G 6 HOH B 76 479 117 HOH HOH . G 6 HOH B 77 480 118 HOH HOH . G 6 HOH B 78 481 119 HOH HOH . G 6 HOH B 79 482 120 HOH HOH . G 6 HOH B 80 483 122 HOH HOH . G 6 HOH B 81 484 127 HOH HOH . G 6 HOH B 82 485 129 HOH HOH . G 6 HOH B 83 486 133 HOH HOH . G 6 HOH B 84 487 134 HOH HOH . G 6 HOH B 85 488 135 HOH HOH . G 6 HOH B 86 489 136 HOH HOH . G 6 HOH B 87 490 138 HOH HOH . G 6 HOH B 88 491 140 HOH HOH . G 6 HOH B 89 492 142 HOH HOH . G 6 HOH B 90 493 143 HOH HOH . G 6 HOH B 91 494 144 HOH HOH . G 6 HOH B 92 495 146 HOH HOH . G 6 HOH B 93 496 147 HOH HOH . G 6 HOH B 94 497 150 HOH HOH . G 6 HOH B 95 498 151 HOH HOH . G 6 HOH B 96 499 152 HOH HOH . G 6 HOH B 97 500 153 HOH HOH . G 6 HOH B 98 501 154 HOH HOH . G 6 HOH B 99 502 158 HOH HOH . G 6 HOH B 100 503 160 HOH HOH . G 6 HOH B 101 504 161 HOH HOH . G 6 HOH B 102 505 162 HOH HOH . G 6 HOH B 103 506 164 HOH HOH . G 6 HOH B 104 507 165 HOH HOH . G 6 HOH B 105 508 166 HOH HOH . G 6 HOH B 106 509 168 HOH HOH . G 6 HOH B 107 510 170 HOH HOH . G 6 HOH B 108 511 174 HOH HOH . G 6 HOH B 109 512 175 HOH HOH . G 6 HOH B 110 513 177 HOH HOH . G 6 HOH B 111 514 179 HOH HOH . G 6 HOH B 112 515 180 HOH HOH . G 6 HOH B 113 516 181 HOH HOH . G 6 HOH B 114 517 182 HOH HOH . G 6 HOH B 115 518 183 HOH HOH . G 6 HOH B 116 519 185 HOH HOH . G 6 HOH B 117 520 186 HOH HOH . G 6 HOH B 118 521 187 HOH HOH . G 6 HOH B 119 522 188 HOH HOH . G 6 HOH B 120 523 189 HOH HOH . G 6 HOH B 121 524 190 HOH HOH . G 6 HOH B 122 525 191 HOH HOH . G 6 HOH B 123 526 192 HOH HOH . G 6 HOH B 124 527 193 HOH HOH . G 6 HOH B 125 528 195 HOH HOH . G 6 HOH B 126 529 196 HOH HOH . G 6 HOH B 127 530 197 HOH HOH . G 6 HOH B 128 531 198 HOH HOH . G 6 HOH B 129 532 199 HOH HOH . G 6 HOH B 130 533 200 HOH HOH . G 6 HOH B 131 534 201 HOH HOH . G 6 HOH B 132 535 202 HOH HOH . G 6 HOH B 133 536 203 HOH HOH . G 6 HOH B 134 537 204 HOH HOH . G 6 HOH B 135 538 205 HOH HOH . G 6 HOH B 136 539 207 HOH HOH . G 6 HOH B 137 540 208 HOH HOH . G 6 HOH B 138 541 209 HOH HOH . G 6 HOH B 139 542 210 HOH HOH . G 6 HOH B 140 543 211 HOH HOH . G 6 HOH B 141 544 212 HOH HOH . G 6 HOH B 142 545 214 HOH HOH . G 6 HOH B 143 546 215 HOH HOH . G 6 HOH B 144 547 220 HOH HOH . G 6 HOH B 145 548 221 HOH HOH . G 6 HOH B 146 549 223 HOH HOH . G 6 HOH B 147 550 226 HOH HOH . G 6 HOH B 148 551 228 HOH HOH . G 6 HOH B 149 552 229 HOH HOH . G 6 HOH B 150 553 230 HOH HOH . G 6 HOH B 151 554 232 HOH HOH . G 6 HOH B 152 555 233 HOH HOH . G 6 HOH B 153 556 234 HOH HOH . G 6 HOH B 154 557 235 HOH HOH . G 6 HOH B 155 558 237 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 84.345 13.775 12.119 1 10.87 ? N1 PLP 402 B 1 HETATM 2 C C2 PLP . . . E 5 84.284 14.19 10.83 1 22.21 ? C2 PLP 402 B 1 HETATM 3 C C2A PLP . . . E 5 85.472 14.052 9.934 1 6.37 ? C2A PLP 402 B 1 HETATM 4 C C3 PLP . . . E 5 83.139 14.687 10.311 1 17.17 ? C3 PLP 402 B 1 HETATM 5 O O3 PLP . . . E 5 83.091 14.992 9.013 1 23.11 ? O3 PLP 402 B 1 HETATM 6 C C4 PLP . . . E 5 82.06 14.736 11.07 1 20.38 ? C4 PLP 402 B 1 HETATM 7 C C4A PLP . . . E 5 80.78 15.302 10.398 1 30.41 ? C4A PLP 402 B 1 HETATM 8 C C5 PLP . . . E 5 82.054 14.409 12.42 1 15.42 ? C5 PLP 402 B 1 HETATM 9 C C6 PLP . . . E 5 83.217 13.908 12.908 1 15.74 ? C6 PLP 402 B 1 HETATM 10 C C5A PLP . . . E 5 80.83 14.673 13.398 1 3.02 ? C5A PLP 402 B 1 HETATM 11 O O4P PLP . . . E 5 79.627 14.079 13.188 1 11.66 ? O4P PLP 402 B 1 HETATM 12 P P PLP . . . E 5 79.522 12.652 13.806 1 12.21 ? P PLP 402 B 1 HETATM 13 O O1P PLP . . . E 5 78.205 12.207 13.561 1 15.13 ? O1P PLP 402 B 1 HETATM 14 O O2P PLP . . . E 5 79.542 13.139 15.22 1 19.35 ? O2P PLP 402 B 1 HETATM 15 O O3P PLP . . . E 5 80.536 11.58 13.492 1 10.97 ? O3P PLP 402 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #