data_3DWI # _model_server_result.job_id ZNFVyM6yoaJRGBZSUMJsqA _model_server_result.datetime_utc '2024-10-15 11:20:16' _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 3dwi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 3DWI # _exptl.entry_id 3DWI _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 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 3DWI _cell.length_a 72.361 _cell.length_b 85.351 _cell.length_c 98.916 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DWI _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 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,F,G,H,I _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 ? 3 D N N ? 3 G 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 51 A LYS 51 1_555 D C4A PLP . A PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.113 ? covale ? covale2 B NZ LYS 51 B LYS 51 1_555 G C4A PLP . B PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? # _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 3DWI _atom_sites.fract_transf_matrix[1][1] 0.01382 _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] 0.011716 _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] 0.01011 _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 SO4 A 1 324 324 SO4 SO4 . D 3 PLP A 1 401 401 PLP PLP . E 2 SO4 B 1 324 324 SO4 SO4 . F 2 SO4 B 1 325 325 SO4 SO4 . G 3 PLP B 1 401 401 PLP PLP . H 4 HOH A 1 402 402 HOH HOH . H 4 HOH A 2 403 403 HOH HOH . H 4 HOH A 3 404 404 HOH HOH . H 4 HOH A 4 405 405 HOH HOH . H 4 HOH A 5 406 406 HOH HOH . H 4 HOH A 6 407 407 HOH HOH . H 4 HOH A 7 408 408 HOH HOH . H 4 HOH A 8 409 409 HOH HOH . H 4 HOH A 9 410 410 HOH HOH . H 4 HOH A 10 411 411 HOH HOH . H 4 HOH A 11 412 412 HOH HOH . H 4 HOH A 12 413 413 HOH HOH . H 4 HOH A 13 414 414 HOH HOH . H 4 HOH A 14 416 416 HOH HOH . H 4 HOH A 15 417 417 HOH HOH . H 4 HOH A 16 418 418 HOH HOH . H 4 HOH A 17 419 419 HOH HOH . H 4 HOH A 18 420 420 HOH HOH . H 4 HOH A 19 421 421 HOH HOH . H 4 HOH A 20 422 422 HOH HOH . H 4 HOH A 21 423 423 HOH HOH . H 4 HOH A 22 424 424 HOH HOH . H 4 HOH A 23 425 425 HOH HOH . H 4 HOH A 24 426 426 HOH HOH . H 4 HOH A 25 427 427 HOH HOH . H 4 HOH A 26 428 428 HOH HOH . H 4 HOH A 27 429 429 HOH HOH . H 4 HOH A 28 430 430 HOH HOH . H 4 HOH A 29 431 431 HOH HOH . H 4 HOH A 30 432 432 HOH HOH . H 4 HOH A 31 433 433 HOH HOH . H 4 HOH A 32 434 434 HOH HOH . H 4 HOH A 33 435 435 HOH HOH . H 4 HOH A 34 436 436 HOH HOH . H 4 HOH A 35 437 437 HOH HOH . H 4 HOH A 36 438 438 HOH HOH . H 4 HOH A 37 439 439 HOH HOH . H 4 HOH A 38 440 440 HOH HOH . H 4 HOH A 39 441 441 HOH HOH . H 4 HOH A 40 442 442 HOH HOH . H 4 HOH A 41 443 443 HOH HOH . H 4 HOH A 42 444 444 HOH HOH . H 4 HOH A 43 445 445 HOH HOH . H 4 HOH A 44 446 446 HOH HOH . H 4 HOH A 45 447 447 HOH HOH . H 4 HOH A 46 448 448 HOH HOH . H 4 HOH A 47 449 449 HOH HOH . H 4 HOH A 48 450 450 HOH HOH . H 4 HOH A 49 451 451 HOH HOH . H 4 HOH A 50 452 452 HOH HOH . H 4 HOH A 51 453 453 HOH HOH . H 4 HOH A 52 454 454 HOH HOH . H 4 HOH A 53 455 455 HOH HOH . H 4 HOH A 54 456 456 HOH HOH . H 4 HOH A 55 457 457 HOH HOH . H 4 HOH A 56 458 458 HOH HOH . H 4 HOH A 57 459 459 HOH HOH . H 4 HOH A 58 460 460 HOH HOH . H 4 HOH A 59 461 461 HOH HOH . H 4 HOH A 60 462 462 HOH HOH . H 4 HOH A 61 463 463 HOH HOH . H 4 HOH A 62 464 464 HOH HOH . H 4 HOH A 63 465 465 HOH HOH . H 4 HOH A 64 466 466 HOH HOH . H 4 HOH A 65 467 467 HOH HOH . H 4 HOH A 66 468 468 HOH HOH . H 4 HOH A 67 469 469 HOH HOH . H 4 HOH A 68 470 470 HOH HOH . H 4 HOH A 69 471 471 HOH HOH . H 4 HOH A 70 472 472 HOH HOH . H 4 HOH A 71 473 473 HOH HOH . H 4 HOH A 72 474 474 HOH HOH . I 4 HOH B 1 415 415 HOH HOH . I 4 HOH B 2 416 416 HOH HOH . I 4 HOH B 3 417 417 HOH HOH . I 4 HOH B 4 418 418 HOH HOH . I 4 HOH B 5 419 419 HOH HOH . I 4 HOH B 6 420 420 HOH HOH . I 4 HOH B 7 421 421 HOH HOH . I 4 HOH B 8 422 422 HOH HOH . I 4 HOH B 9 423 423 HOH HOH . I 4 HOH B 10 424 424 HOH HOH . I 4 HOH B 11 425 425 HOH HOH . I 4 HOH B 12 426 426 HOH HOH . I 4 HOH B 13 427 427 HOH HOH . I 4 HOH B 14 428 428 HOH HOH . I 4 HOH B 15 429 429 HOH HOH . I 4 HOH B 16 430 430 HOH HOH . I 4 HOH B 17 431 431 HOH HOH . I 4 HOH B 18 432 432 HOH HOH . I 4 HOH B 19 433 433 HOH HOH . I 4 HOH B 20 434 434 HOH HOH . I 4 HOH B 21 435 435 HOH HOH . I 4 HOH B 22 436 436 HOH HOH . I 4 HOH B 23 437 437 HOH HOH . I 4 HOH B 24 438 438 HOH HOH . I 4 HOH B 25 439 439 HOH HOH . I 4 HOH B 26 440 440 HOH HOH . I 4 HOH B 27 441 441 HOH HOH . I 4 HOH B 28 442 442 HOH HOH . I 4 HOH B 29 443 443 HOH HOH . I 4 HOH B 30 444 444 HOH HOH . I 4 HOH B 31 445 445 HOH HOH . I 4 HOH B 32 446 446 HOH HOH . I 4 HOH B 33 447 447 HOH HOH . I 4 HOH B 34 448 448 HOH HOH . I 4 HOH B 35 449 449 HOH HOH . I 4 HOH B 36 450 450 HOH HOH . I 4 HOH B 37 451 451 HOH HOH . I 4 HOH B 38 452 452 HOH HOH . I 4 HOH B 39 453 453 HOH HOH . I 4 HOH B 40 454 454 HOH HOH . I 4 HOH B 41 455 455 HOH HOH . I 4 HOH B 42 456 456 HOH HOH . I 4 HOH B 43 457 457 HOH HOH . I 4 HOH B 44 458 458 HOH HOH . I 4 HOH B 45 459 459 HOH HOH . I 4 HOH B 46 460 460 HOH HOH . I 4 HOH B 47 461 461 HOH HOH . I 4 HOH B 48 462 462 HOH HOH . I 4 HOH B 49 463 463 HOH HOH . I 4 HOH B 50 464 464 HOH HOH . I 4 HOH B 51 465 465 HOH HOH . I 4 HOH B 52 466 466 HOH HOH . I 4 HOH B 53 467 467 HOH HOH . I 4 HOH B 54 468 468 HOH HOH . I 4 HOH B 55 469 469 HOH HOH . I 4 HOH B 56 470 470 HOH HOH . I 4 HOH B 57 471 471 HOH HOH . I 4 HOH B 58 472 472 HOH HOH . I 4 HOH B 59 473 473 HOH HOH . I 4 HOH B 60 474 474 HOH HOH . I 4 HOH B 61 475 475 HOH HOH . I 4 HOH B 62 476 476 HOH HOH . I 4 HOH B 63 477 477 HOH HOH . I 4 HOH B 64 478 478 HOH HOH . I 4 HOH B 65 479 479 HOH HOH . I 4 HOH B 66 480 480 HOH HOH . I 4 HOH B 67 481 481 HOH HOH . I 4 HOH B 68 482 482 HOH HOH . I 4 HOH B 69 483 483 HOH HOH . I 4 HOH B 70 484 484 HOH HOH . I 4 HOH B 71 485 485 HOH HOH . I 4 HOH B 72 486 486 HOH HOH . I 4 HOH B 73 487 487 HOH HOH . I 4 HOH B 74 488 488 HOH HOH . I 4 HOH B 75 489 489 HOH HOH . I 4 HOH B 76 490 490 HOH HOH . I 4 HOH B 77 491 491 HOH HOH . I 4 HOH B 78 492 492 HOH HOH . I 4 HOH B 79 493 493 HOH HOH . I 4 HOH B 80 494 494 HOH HOH . I 4 HOH B 81 495 495 HOH HOH . I 4 HOH B 82 496 496 HOH HOH . I 4 HOH B 83 497 497 HOH HOH . I 4 HOH B 84 498 498 HOH HOH . I 4 HOH B 85 499 499 HOH HOH . I 4 HOH B 86 500 500 HOH HOH . I 4 HOH B 87 501 501 HOH HOH . I 4 HOH B 88 502 502 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 3 20.389 82.27 21.006 1 15.34 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . D 3 20.913 81.12 21.283 1 15.94 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . D 3 22.137 81.021 22.075 1 12.77 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . D 3 20.322 79.993 20.85 1 19.11 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . D 3 20.788 78.794 21.1 1 24.95 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . D 3 19.211 80.008 20.134 1 18.88 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . D 3 18.771 78.74 19.805 1 15.71 ? C4A PLP 401 A 1 HETATM 8 C C5 PLP . . . D 3 18.66 81.23 19.836 1 17.04 ? C5 PLP 401 A 1 HETATM 9 C C6 PLP . . . D 3 19.304 82.327 20.289 1 15.96 ? C6 PLP 401 A 1 HETATM 10 C C5A PLP . . . D 3 17.429 81.53 19.035 1 18.15 ? C5A PLP 401 A 1 HETATM 11 O O4P PLP . . . D 3 16.353 80.863 19.492 1 19.02 ? O4P PLP 401 A 1 HETATM 12 P P PLP . . . D 3 15.307 80.395 18.726 1 18.35 ? P PLP 401 A 1 HETATM 13 O O1P PLP . . . D 3 14.478 81.294 18.131 1 12.78 ? O1P PLP 401 A 1 HETATM 14 O O2P PLP . . . D 3 14.514 79.923 19.595 1 21.18 ? O2P PLP 401 A 1 HETATM 15 O O3P PLP . . . D 3 15.448 79.193 18.228 1 21.34 ? O3P PLP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #