data_3L6B # _model_server_result.job_id 5iQkIZmtYxWhMGYVcQb22g _model_server_result.datetime_utc '2024-11-08 18:00:09' _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 3l6b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":350}' # _entry.id 3L6B # _exptl.entry_id 3L6B _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 1 _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 3L6B _cell.length_a 54.57 _cell.length_b 84.29 _cell.length_c 69.98 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L6B _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 84.29 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 A NZ LYS 56 A LYS 56 1_555 B C4A PLP . A PLP 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.539 ? metalc ? metalc1 A OE2 GLU 210 A GLU 210 1_555 C MN MN . A MN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A O ALA 214 A ALA 214 1_555 C MN MN . A MN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc3 A OD1 ASP 216 A ASP 216 1_555 C MN MN . A MN 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc4 C MN MN . A MN 347 1_555 E O HOH . A HOH 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc5 C MN MN . A MN 347 1_555 E O HOH . A HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc6 C MN MN . A MN 347 1_555 E O HOH . A HOH 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? # _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 268 n y N1 C6 PLP sing 269 n y C2 C2A PLP sing 270 n n C2 C3 PLP sing 271 n y C2A H2A1 PLP sing 272 n n C2A H2A2 PLP sing 273 n n C2A H2A3 PLP sing 274 n n C3 O3 PLP sing 275 n n C3 C4 PLP doub 276 n y O3 HO3 PLP sing 277 n n C4 C4A PLP sing 278 n n C4 C5 PLP sing 279 n y C4A O4A PLP doub 280 n n C4A H4A PLP sing 281 n n C5 C6 PLP doub 282 n y C5 C5A PLP sing 283 n n C6 H6 PLP sing 284 n n C5A O4P PLP sing 285 n n C5A H5A1 PLP sing 286 n n C5A H5A2 PLP sing 287 n n O4P P PLP sing 288 n n P O1P PLP doub 289 n n P O2P PLP sing 290 n n P O3P PLP sing 291 n n O2P HOP2 PLP sing 292 n n O3P HOP3 PLP sing 293 n n # _atom_sites.entry_id 3L6B _atom_sites.fract_transf_matrix[1][1] 0.018325 _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] 0.011864 _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] 0.01429 _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 B 2 PLP A 1 350 350 PLP PLP . C 3 MN A 1 347 347 MN MN . D 4 MLI A 1 348 348 MLI MLI . E 5 HOH A 1 349 349 HOH HOH . E 5 HOH A 2 351 351 HOH HOH . E 5 HOH A 3 352 352 HOH HOH . E 5 HOH A 4 353 353 HOH HOH . E 5 HOH A 5 354 354 HOH HOH . E 5 HOH A 6 355 355 HOH HOH . E 5 HOH A 7 356 356 HOH HOH . E 5 HOH A 8 357 357 HOH HOH . E 5 HOH A 9 358 358 HOH HOH . E 5 HOH A 10 359 359 HOH HOH . E 5 HOH A 11 360 360 HOH HOH . E 5 HOH A 12 361 361 HOH HOH . E 5 HOH A 13 362 362 HOH HOH . E 5 HOH A 14 363 363 HOH HOH . E 5 HOH A 15 364 364 HOH HOH . E 5 HOH A 16 365 365 HOH HOH . E 5 HOH A 17 366 366 HOH HOH . E 5 HOH A 18 367 367 HOH HOH . E 5 HOH A 19 368 368 HOH HOH . E 5 HOH A 20 369 369 HOH HOH . E 5 HOH A 21 370 370 HOH HOH . E 5 HOH A 22 371 371 HOH HOH . E 5 HOH A 23 372 372 HOH HOH . E 5 HOH A 24 373 373 HOH HOH . E 5 HOH A 25 374 374 HOH HOH . E 5 HOH A 26 375 375 HOH HOH . E 5 HOH A 27 376 376 HOH HOH . E 5 HOH A 28 377 377 HOH HOH . E 5 HOH A 29 378 378 HOH HOH . E 5 HOH A 30 379 379 HOH HOH . E 5 HOH A 31 380 380 HOH HOH . E 5 HOH A 32 381 381 HOH HOH . E 5 HOH A 33 382 382 HOH HOH . E 5 HOH A 34 383 383 HOH HOH . E 5 HOH A 35 384 384 HOH HOH . E 5 HOH A 36 385 385 HOH HOH . E 5 HOH A 37 386 386 HOH HOH . E 5 HOH A 38 387 387 HOH HOH . E 5 HOH A 39 388 388 HOH HOH . E 5 HOH A 40 389 389 HOH HOH . E 5 HOH A 41 390 390 HOH HOH . E 5 HOH A 42 391 391 HOH HOH . E 5 HOH A 43 392 392 HOH HOH . E 5 HOH A 44 393 393 HOH HOH . E 5 HOH A 45 394 394 HOH HOH . E 5 HOH A 46 395 395 HOH HOH . E 5 HOH A 47 396 396 HOH HOH . E 5 HOH A 48 397 397 HOH HOH . E 5 HOH A 49 398 398 HOH HOH . E 5 HOH A 50 399 399 HOH HOH . E 5 HOH A 51 400 400 HOH HOH . E 5 HOH A 52 401 401 HOH HOH . E 5 HOH A 53 402 402 HOH HOH . E 5 HOH A 54 403 403 HOH HOH . E 5 HOH A 55 404 404 HOH HOH . E 5 HOH A 56 405 405 HOH HOH . E 5 HOH A 57 406 406 HOH HOH . E 5 HOH A 58 407 407 HOH HOH . E 5 HOH A 59 408 408 HOH HOH . E 5 HOH A 60 409 409 HOH HOH . E 5 HOH A 61 410 410 HOH HOH . E 5 HOH A 62 411 411 HOH HOH . E 5 HOH A 63 412 412 HOH HOH . E 5 HOH A 64 413 413 HOH HOH . E 5 HOH A 65 414 414 HOH HOH . E 5 HOH A 66 415 415 HOH HOH . E 5 HOH A 67 416 416 HOH HOH . E 5 HOH A 68 417 417 HOH HOH . E 5 HOH A 69 418 418 HOH HOH . E 5 HOH A 70 419 419 HOH HOH . E 5 HOH A 71 420 420 HOH HOH . E 5 HOH A 72 421 421 HOH HOH . E 5 HOH A 73 422 422 HOH HOH . E 5 HOH A 74 423 423 HOH HOH . E 5 HOH A 75 424 424 HOH HOH . E 5 HOH A 76 425 425 HOH HOH . E 5 HOH A 77 426 426 HOH HOH . E 5 HOH A 78 427 427 HOH HOH . E 5 HOH A 79 428 428 HOH HOH . E 5 HOH A 80 429 429 HOH HOH . E 5 HOH A 81 430 430 HOH HOH . E 5 HOH A 82 431 431 HOH HOH . E 5 HOH A 83 432 432 HOH HOH . E 5 HOH A 84 433 433 HOH HOH . E 5 HOH A 85 434 434 HOH HOH . E 5 HOH A 86 435 435 HOH HOH . E 5 HOH A 87 436 436 HOH HOH . E 5 HOH A 88 437 437 HOH HOH . E 5 HOH A 89 438 438 HOH HOH . E 5 HOH A 90 439 439 HOH HOH . E 5 HOH A 91 440 440 HOH HOH . E 5 HOH A 92 441 441 HOH HOH . E 5 HOH A 93 442 442 HOH HOH . E 5 HOH A 94 443 443 HOH HOH . E 5 HOH A 95 444 444 HOH HOH . E 5 HOH A 96 445 445 HOH HOH . E 5 HOH A 97 446 446 HOH HOH . E 5 HOH A 98 447 447 HOH HOH . E 5 HOH A 99 448 448 HOH HOH . E 5 HOH A 100 449 449 HOH HOH . E 5 HOH A 101 450 450 HOH HOH . E 5 HOH A 102 451 451 HOH HOH . E 5 HOH A 103 452 452 HOH HOH . E 5 HOH A 104 453 453 HOH HOH . E 5 HOH A 105 454 454 HOH HOH . E 5 HOH A 106 455 455 HOH HOH . E 5 HOH A 107 456 456 HOH HOH . E 5 HOH A 108 457 457 HOH HOH . E 5 HOH A 109 458 458 HOH HOH . E 5 HOH A 110 459 459 HOH HOH . E 5 HOH A 111 460 460 HOH HOH . E 5 HOH A 112 461 461 HOH HOH . E 5 HOH A 113 462 462 HOH HOH . E 5 HOH A 114 463 463 HOH HOH . E 5 HOH A 115 464 464 HOH HOH . E 5 HOH A 116 465 465 HOH HOH . E 5 HOH A 117 466 466 HOH HOH . E 5 HOH A 118 467 467 HOH HOH . E 5 HOH A 119 468 468 HOH HOH . E 5 HOH A 120 469 469 HOH HOH . E 5 HOH A 121 470 470 HOH HOH . E 5 HOH A 122 471 471 HOH HOH . E 5 HOH A 123 472 472 HOH HOH . E 5 HOH A 124 473 473 HOH HOH . E 5 HOH A 125 474 474 HOH HOH . E 5 HOH A 126 475 475 HOH HOH . E 5 HOH A 127 476 476 HOH HOH . E 5 HOH A 128 477 477 HOH HOH . E 5 HOH A 129 478 478 HOH HOH . E 5 HOH A 130 479 479 HOH HOH . E 5 HOH A 131 480 480 HOH HOH . E 5 HOH A 132 481 481 HOH HOH . E 5 HOH A 133 482 482 HOH HOH . E 5 HOH A 134 483 483 HOH HOH . E 5 HOH A 135 484 484 HOH HOH . E 5 HOH A 136 485 485 HOH HOH . E 5 HOH A 137 486 486 HOH HOH . E 5 HOH A 138 487 487 HOH HOH . E 5 HOH A 139 488 488 HOH HOH . E 5 HOH A 140 489 489 HOH HOH . E 5 HOH A 141 490 490 HOH HOH . E 5 HOH A 142 491 491 HOH HOH . E 5 HOH A 143 492 492 HOH HOH . E 5 HOH A 144 493 493 HOH HOH . E 5 HOH A 145 494 494 HOH HOH . E 5 HOH A 146 495 495 HOH HOH . E 5 HOH A 147 496 496 HOH HOH . E 5 HOH A 148 497 497 HOH HOH . E 5 HOH A 149 498 498 HOH HOH . E 5 HOH A 150 499 499 HOH HOH . E 5 HOH A 151 500 500 HOH HOH . E 5 HOH A 152 502 502 HOH HOH . E 5 HOH A 153 503 503 HOH HOH . E 5 HOH A 154 504 504 HOH HOH . E 5 HOH A 155 505 505 HOH HOH . E 5 HOH A 156 506 506 HOH HOH . E 5 HOH A 157 507 507 HOH HOH . E 5 HOH A 158 508 508 HOH HOH . E 5 HOH A 159 509 509 HOH HOH . E 5 HOH A 160 510 510 HOH HOH . E 5 HOH A 161 511 511 HOH HOH . E 5 HOH A 162 512 512 HOH HOH . E 5 HOH A 163 513 513 HOH HOH . E 5 HOH A 164 514 514 HOH HOH . E 5 HOH A 165 515 515 HOH HOH . E 5 HOH A 166 516 516 HOH HOH . E 5 HOH A 167 517 517 HOH HOH . E 5 HOH A 168 518 518 HOH HOH . E 5 HOH A 169 519 519 HOH HOH . E 5 HOH A 170 520 520 HOH HOH . E 5 HOH A 171 521 521 HOH HOH . E 5 HOH A 172 522 522 HOH HOH . E 5 HOH A 173 523 523 HOH HOH . E 5 HOH A 174 524 524 HOH HOH . E 5 HOH A 175 525 525 HOH HOH . E 5 HOH A 176 526 526 HOH HOH . E 5 HOH A 177 527 527 HOH HOH . E 5 HOH A 178 528 528 HOH HOH . E 5 HOH A 179 529 529 HOH HOH . E 5 HOH A 180 530 530 HOH HOH . E 5 HOH A 181 531 531 HOH HOH . E 5 HOH A 182 532 532 HOH HOH . E 5 HOH A 183 533 533 HOH HOH . E 5 HOH A 184 534 534 HOH HOH . E 5 HOH A 185 535 535 HOH HOH . E 5 HOH A 186 536 536 HOH HOH . E 5 HOH A 187 537 537 HOH HOH . E 5 HOH A 188 538 538 HOH HOH . E 5 HOH A 189 539 539 HOH HOH . E 5 HOH A 190 540 540 HOH HOH . E 5 HOH A 191 541 541 HOH HOH . E 5 HOH A 192 542 542 HOH HOH . E 5 HOH A 193 543 543 HOH HOH . E 5 HOH A 194 544 544 HOH HOH . E 5 HOH A 195 545 545 HOH HOH . E 5 HOH A 196 546 546 HOH HOH . E 5 HOH A 197 547 547 HOH HOH . E 5 HOH A 198 548 548 HOH HOH . E 5 HOH A 199 550 550 HOH HOH . E 5 HOH A 200 551 551 HOH HOH . E 5 HOH A 201 552 552 HOH HOH . E 5 HOH A 202 553 553 HOH HOH . E 5 HOH A 203 554 554 HOH HOH . E 5 HOH A 204 555 555 HOH HOH . E 5 HOH A 205 556 556 HOH HOH . E 5 HOH A 206 557 557 HOH HOH . E 5 HOH A 207 559 559 HOH HOH . E 5 HOH A 208 560 560 HOH HOH . E 5 HOH A 209 561 561 HOH HOH . E 5 HOH A 210 562 562 HOH HOH . E 5 HOH A 211 563 563 HOH HOH . E 5 HOH A 212 564 564 HOH HOH . E 5 HOH A 213 565 565 HOH HOH . E 5 HOH A 214 566 566 HOH HOH . E 5 HOH A 215 567 567 HOH HOH . E 5 HOH A 216 568 568 HOH HOH . E 5 HOH A 217 569 569 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 . . . B 2 -2.127 26.276 -20.947 1 8.98 ? N1 PLP 350 A 1 HETATM 2 C C2 PLP . . . B 2 -0.81 26.448 -21.16 1 8.55 ? C2 PLP 350 A 1 HETATM 3 C C2A PLP . . . B 2 -0.282 27.828 -21.467 1 9.42 ? C2A PLP 350 A 1 HETATM 4 C C3 PLP . . . B 2 0.048 25.361 -21.064 1 7.98 ? C3 PLP 350 A 1 HETATM 5 O O3 PLP . . . B 2 1.378 25.543 -21.278 1 10.43 ? O3 PLP 350 A 1 HETATM 6 C C4 PLP . . . B 2 -0.482 24.095 -20.788 1 6.97 ? C4 PLP 350 A 1 HETATM 7 C C4A PLP . . . B 2 0.397 22.898 -20.659 1 9.77 ? C4A PLP 350 A 1 HETATM 8 C C5 PLP . . . B 2 -1.842 23.941 -20.588 1 7.57 ? C5 PLP 350 A 1 HETATM 9 C C6 PLP . . . B 2 -2.647 25.069 -20.672 1 8.72 ? C6 PLP 350 A 1 HETATM 10 C C5A PLP . . . B 2 -2.472 22.582 -20.318 1 8.47 ? C5A PLP 350 A 1 HETATM 11 O O4P PLP . . . B 2 -1.896 21.828 -19.249 1 8.59 ? O4P PLP 350 A 1 HETATM 12 P P PLP . . . B 2 -1.99 20.225 -19.321 1 9.33 ? P PLP 350 A 1 HETATM 13 O O1P PLP . . . B 2 -1.226 19.781 -20.558 1 10.12 ? O1P PLP 350 A 1 HETATM 14 O O2P PLP . . . B 2 -3.461 19.92 -19.422 1 9.68 ? O2P PLP 350 A 1 HETATM 15 O O3P PLP . . . B 2 -1.356 19.763 -18.037 1 9.61 ? O3P PLP 350 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #