data_1BKG # _model_server_result.job_id ghY0ECt1FebnqcYEIWhnYQ _model_server_result.datetime_utc '2024-11-02 11:22:12' _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 1bkg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":413}' # _entry.id 1BKG # _exptl.entry_id 1BKG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.173 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 1BKG _cell.length_a 80.25 _cell.length_b 109.71 _cell.length_c 197.3 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BKG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 E N N ? 2 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C8 H13 N2 O5 P' _chem_comp.formula_weight 248.173 _chem_comp.id PMP _chem_comp.mon_nstd_flag . _chem_comp.name "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "PYRIDOXAMINE-5'-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 PMP doub 271 n y N1 C6 PMP sing 272 n y C2 C2A PMP sing 273 n n C2 C3 PMP sing 274 n y C2A H2A1 PMP sing 275 n n C2A H2A2 PMP sing 276 n n C2A H2A3 PMP sing 277 n n C3 O3 PMP sing 278 n n C3 C4 PMP doub 279 n y O3 HO3 PMP sing 280 n n C4 C4A PMP sing 281 n n C4 C5 PMP sing 282 n y C4A N4A PMP sing 283 n n C4A H4A1 PMP sing 284 n n C4A H4A2 PMP sing 285 n n N4A HNA1 PMP sing 286 n n N4A HNA2 PMP sing 287 n n C5 C6 PMP doub 288 n y C5 C5A PMP sing 289 n n C6 H6 PMP sing 290 n n C5A O4P PMP sing 291 n n C5A H5A1 PMP sing 292 n n C5A H5A2 PMP sing 293 n n O4P P PMP sing 294 n n P O1P PMP doub 295 n n P O2P PMP sing 296 n n P O3P PMP sing 297 n n O2P HOP2 PMP sing 298 n n O3P HOP3 PMP sing 299 n n # _atom_sites.entry_id 1BKG _atom_sites.fract_transf_matrix[1][1] 0.012461 _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] 0.009115 _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] 0.005068 _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 E 2 PMP A 1 413 413 PMP PMP . F 3 MAE A 1 414 414 MAE MAE . G 2 PMP B 1 413 413 PMP PMP . H 3 MAE B 1 414 414 MAE MAE . I 2 PMP C 1 413 413 PMP PMP . J 3 MAE C 1 414 414 MAE MAE . K 2 PMP D 1 413 413 PMP PMP . L 3 MAE D 1 414 414 MAE MAE . M 4 HOH A 1 501 501 HOH HOH . M 4 HOH A 2 502 502 HOH HOH . M 4 HOH A 3 503 504 HOH HOH . M 4 HOH A 4 504 505 HOH HOH . M 4 HOH A 5 505 506 HOH HOH . M 4 HOH A 6 506 507 HOH HOH . M 4 HOH A 7 507 508 HOH HOH . M 4 HOH A 8 508 509 HOH HOH . M 4 HOH A 9 509 512 HOH HOH . M 4 HOH A 10 510 514 HOH HOH . M 4 HOH A 11 511 515 HOH HOH . M 4 HOH A 12 512 516 HOH HOH . M 4 HOH A 13 513 519 HOH HOH . M 4 HOH A 14 514 521 HOH HOH . M 4 HOH A 15 515 523 HOH HOH . M 4 HOH A 16 516 524 HOH HOH . M 4 HOH A 17 517 525 HOH HOH . M 4 HOH A 18 518 526 HOH HOH . M 4 HOH A 19 519 527 HOH HOH . M 4 HOH A 20 520 529 HOH HOH . M 4 HOH A 21 521 530 HOH HOH . M 4 HOH A 22 522 533 HOH HOH . M 4 HOH A 23 523 536 HOH HOH . M 4 HOH A 24 524 537 HOH HOH . M 4 HOH A 25 525 539 HOH HOH . M 4 HOH A 26 526 540 HOH HOH . M 4 HOH A 27 527 541 HOH HOH . M 4 HOH A 28 528 542 HOH HOH . M 4 HOH A 29 529 543 HOH HOH . M 4 HOH A 30 530 544 HOH HOH . M 4 HOH A 31 531 545 HOH HOH . M 4 HOH A 32 532 548 HOH HOH . M 4 HOH A 33 533 550 HOH HOH . M 4 HOH A 34 534 552 HOH HOH . M 4 HOH A 35 535 553 HOH HOH . M 4 HOH A 36 536 555 HOH HOH . M 4 HOH A 37 537 556 HOH HOH . M 4 HOH A 38 538 558 HOH HOH . M 4 HOH A 39 539 559 HOH HOH . M 4 HOH A 40 540 560 HOH HOH . M 4 HOH A 41 541 561 HOH HOH . M 4 HOH A 42 542 562 HOH HOH . M 4 HOH A 43 543 563 HOH HOH . M 4 HOH A 44 544 564 HOH HOH . M 4 HOH A 45 545 565 HOH HOH . M 4 HOH A 46 546 566 HOH HOH . M 4 HOH A 47 547 567 HOH HOH . M 4 HOH A 48 548 569 HOH HOH . M 4 HOH A 49 549 570 HOH HOH . M 4 HOH A 50 550 571 HOH HOH . M 4 HOH A 51 551 572 HOH HOH . M 4 HOH A 52 552 573 HOH HOH . M 4 HOH A 53 553 574 HOH HOH . M 4 HOH A 54 554 575 HOH HOH . M 4 HOH A 55 555 503 HOH HOH . M 4 HOH A 56 556 510 HOH HOH . M 4 HOH A 57 557 511 HOH HOH . M 4 HOH A 58 558 518 HOH HOH . M 4 HOH A 59 559 522 HOH HOH . M 4 HOH A 60 560 528 HOH HOH . M 4 HOH A 61 561 532 HOH HOH . M 4 HOH A 62 562 534 HOH HOH . M 4 HOH A 63 563 535 HOH HOH . M 4 HOH A 64 564 546 HOH HOH . M 4 HOH A 65 565 547 HOH HOH . M 4 HOH A 66 566 551 HOH HOH . M 4 HOH A 67 567 554 HOH HOH . M 4 HOH A 68 568 557 HOH HOH . M 4 HOH A 69 569 536 HOH HOH . M 4 HOH A 70 570 538 HOH HOH . M 4 HOH A 71 571 513 HOH HOH . M 4 HOH A 72 572 532 HOH HOH . N 4 HOH B 1 501 501 HOH HOH . N 4 HOH B 2 502 502 HOH HOH . N 4 HOH B 3 503 503 HOH HOH . N 4 HOH B 4 504 504 HOH HOH . N 4 HOH B 5 505 505 HOH HOH . N 4 HOH B 6 506 506 HOH HOH . N 4 HOH B 7 507 507 HOH HOH . N 4 HOH B 8 508 508 HOH HOH . N 4 HOH B 9 509 509 HOH HOH . N 4 HOH B 10 510 510 HOH HOH . N 4 HOH B 11 511 511 HOH HOH . N 4 HOH B 12 512 512 HOH HOH . N 4 HOH B 13 513 513 HOH HOH . N 4 HOH B 14 514 514 HOH HOH . N 4 HOH B 15 515 515 HOH HOH . N 4 HOH B 16 516 516 HOH HOH . N 4 HOH B 17 518 518 HOH HOH . N 4 HOH B 18 519 519 HOH HOH . N 4 HOH B 19 521 521 HOH HOH . N 4 HOH B 20 522 522 HOH HOH . N 4 HOH B 21 523 523 HOH HOH . N 4 HOH B 22 524 524 HOH HOH . N 4 HOH B 23 525 525 HOH HOH . N 4 HOH B 24 526 526 HOH HOH . N 4 HOH B 25 527 527 HOH HOH . N 4 HOH B 26 528 528 HOH HOH . N 4 HOH B 27 529 529 HOH HOH . N 4 HOH B 28 530 530 HOH HOH . N 4 HOH B 29 532 532 HOH HOH . N 4 HOH B 30 533 533 HOH HOH . N 4 HOH B 31 534 534 HOH HOH . N 4 HOH B 32 535 535 HOH HOH . N 4 HOH B 33 537 537 HOH HOH . N 4 HOH B 34 538 538 HOH HOH . N 4 HOH B 35 539 539 HOH HOH . N 4 HOH B 36 540 540 HOH HOH . N 4 HOH B 37 541 541 HOH HOH . N 4 HOH B 38 542 542 HOH HOH . N 4 HOH B 39 543 543 HOH HOH . N 4 HOH B 40 544 544 HOH HOH . N 4 HOH B 41 545 545 HOH HOH . N 4 HOH B 42 546 546 HOH HOH . N 4 HOH B 43 547 547 HOH HOH . N 4 HOH B 44 548 548 HOH HOH . N 4 HOH B 45 550 550 HOH HOH . N 4 HOH B 46 551 551 HOH HOH . N 4 HOH B 47 552 552 HOH HOH . N 4 HOH B 48 553 553 HOH HOH . N 4 HOH B 49 554 554 HOH HOH . N 4 HOH B 50 555 555 HOH HOH . N 4 HOH B 51 556 556 HOH HOH . N 4 HOH B 52 557 557 HOH HOH . N 4 HOH B 53 558 558 HOH HOH . N 4 HOH B 54 559 559 HOH HOH . N 4 HOH B 55 560 560 HOH HOH . N 4 HOH B 56 561 561 HOH HOH . N 4 HOH B 57 562 562 HOH HOH . N 4 HOH B 58 563 563 HOH HOH . N 4 HOH B 59 564 564 HOH HOH . N 4 HOH B 60 565 565 HOH HOH . N 4 HOH B 61 566 566 HOH HOH . N 4 HOH B 62 567 567 HOH HOH . N 4 HOH B 63 569 569 HOH HOH . N 4 HOH B 64 570 570 HOH HOH . N 4 HOH B 65 571 571 HOH HOH . N 4 HOH B 66 572 572 HOH HOH . N 4 HOH B 67 573 573 HOH HOH . N 4 HOH B 68 574 574 HOH HOH . N 4 HOH B 69 575 575 HOH HOH . O 4 HOH C 1 501 501 HOH HOH . O 4 HOH C 2 502 502 HOH HOH . O 4 HOH C 3 503 503 HOH HOH . O 4 HOH C 4 504 504 HOH HOH . O 4 HOH C 5 505 505 HOH HOH . O 4 HOH C 6 506 506 HOH HOH . O 4 HOH C 7 507 507 HOH HOH . O 4 HOH C 8 508 508 HOH HOH . O 4 HOH C 9 509 509 HOH HOH . O 4 HOH C 10 510 510 HOH HOH . O 4 HOH C 11 511 511 HOH HOH . O 4 HOH C 12 512 512 HOH HOH . O 4 HOH C 13 513 513 HOH HOH . O 4 HOH C 14 514 514 HOH HOH . O 4 HOH C 15 515 515 HOH HOH . O 4 HOH C 16 516 516 HOH HOH . O 4 HOH C 17 518 518 HOH HOH . O 4 HOH C 18 519 519 HOH HOH . O 4 HOH C 19 521 521 HOH HOH . O 4 HOH C 20 522 522 HOH HOH . O 4 HOH C 21 523 523 HOH HOH . O 4 HOH C 22 524 524 HOH HOH . O 4 HOH C 23 525 525 HOH HOH . O 4 HOH C 24 526 526 HOH HOH . O 4 HOH C 25 527 527 HOH HOH . O 4 HOH C 26 528 528 HOH HOH . O 4 HOH C 27 529 529 HOH HOH . O 4 HOH C 28 530 530 HOH HOH . O 4 HOH C 29 533 533 HOH HOH . O 4 HOH C 30 534 534 HOH HOH . O 4 HOH C 31 535 535 HOH HOH . O 4 HOH C 32 537 537 HOH HOH . O 4 HOH C 33 538 538 HOH HOH . O 4 HOH C 34 539 539 HOH HOH . O 4 HOH C 35 540 540 HOH HOH . O 4 HOH C 36 541 541 HOH HOH . O 4 HOH C 37 542 542 HOH HOH . O 4 HOH C 38 543 543 HOH HOH . O 4 HOH C 39 544 544 HOH HOH . O 4 HOH C 40 545 545 HOH HOH . O 4 HOH C 41 546 546 HOH HOH . O 4 HOH C 42 547 547 HOH HOH . O 4 HOH C 43 548 548 HOH HOH . O 4 HOH C 44 550 550 HOH HOH . O 4 HOH C 45 551 551 HOH HOH . O 4 HOH C 46 552 552 HOH HOH . O 4 HOH C 47 553 553 HOH HOH . O 4 HOH C 48 554 554 HOH HOH . O 4 HOH C 49 555 555 HOH HOH . O 4 HOH C 50 556 556 HOH HOH . O 4 HOH C 51 557 557 HOH HOH . O 4 HOH C 52 558 558 HOH HOH . O 4 HOH C 53 559 559 HOH HOH . O 4 HOH C 54 560 560 HOH HOH . O 4 HOH C 55 561 561 HOH HOH . O 4 HOH C 56 562 562 HOH HOH . O 4 HOH C 57 563 563 HOH HOH . O 4 HOH C 58 564 564 HOH HOH . O 4 HOH C 59 565 565 HOH HOH . O 4 HOH C 60 566 566 HOH HOH . O 4 HOH C 61 567 567 HOH HOH . O 4 HOH C 62 569 569 HOH HOH . O 4 HOH C 63 570 570 HOH HOH . O 4 HOH C 64 571 571 HOH HOH . O 4 HOH C 65 572 572 HOH HOH . O 4 HOH C 66 573 573 HOH HOH . O 4 HOH C 67 574 574 HOH HOH . O 4 HOH C 68 575 575 HOH HOH . P 4 HOH D 1 513 513 HOH HOH . P 4 HOH D 2 514 536 HOH HOH . P 4 HOH D 3 515 538 HOH HOH . P 4 HOH D 4 516 503 HOH HOH . P 4 HOH D 5 517 510 HOH HOH . P 4 HOH D 6 518 511 HOH HOH . P 4 HOH D 7 519 518 HOH HOH . P 4 HOH D 8 520 522 HOH HOH . P 4 HOH D 9 521 528 HOH HOH . P 4 HOH D 10 522 532 HOH HOH . P 4 HOH D 11 523 534 HOH HOH . P 4 HOH D 12 524 535 HOH HOH . P 4 HOH D 13 525 546 HOH HOH . P 4 HOH D 14 526 547 HOH HOH . P 4 HOH D 15 527 551 HOH HOH . P 4 HOH D 16 528 554 HOH HOH . P 4 HOH D 17 529 557 HOH HOH . P 4 HOH D 18 530 501 HOH HOH . P 4 HOH D 19 531 502 HOH HOH . P 4 HOH D 20 532 504 HOH HOH . P 4 HOH D 21 533 505 HOH HOH . P 4 HOH D 22 534 506 HOH HOH . P 4 HOH D 23 535 507 HOH HOH . P 4 HOH D 24 536 508 HOH HOH . P 4 HOH D 25 537 509 HOH HOH . P 4 HOH D 26 538 512 HOH HOH . P 4 HOH D 27 539 514 HOH HOH . P 4 HOH D 28 540 515 HOH HOH . P 4 HOH D 29 541 516 HOH HOH . P 4 HOH D 30 542 519 HOH HOH . P 4 HOH D 31 543 521 HOH HOH . P 4 HOH D 32 544 523 HOH HOH . P 4 HOH D 33 545 524 HOH HOH . P 4 HOH D 34 546 525 HOH HOH . P 4 HOH D 35 547 526 HOH HOH . P 4 HOH D 36 548 527 HOH HOH . P 4 HOH D 37 549 529 HOH HOH . P 4 HOH D 38 550 530 HOH HOH . P 4 HOH D 39 551 533 HOH HOH . P 4 HOH D 40 552 536 HOH HOH . P 4 HOH D 41 553 537 HOH HOH . P 4 HOH D 42 554 539 HOH HOH . P 4 HOH D 43 555 540 HOH HOH . P 4 HOH D 44 556 541 HOH HOH . P 4 HOH D 45 557 542 HOH HOH . P 4 HOH D 46 558 543 HOH HOH . P 4 HOH D 47 559 544 HOH HOH . P 4 HOH D 48 560 545 HOH HOH . P 4 HOH D 49 561 548 HOH HOH . P 4 HOH D 50 562 550 HOH HOH . P 4 HOH D 51 563 552 HOH HOH . P 4 HOH D 52 564 553 HOH HOH . P 4 HOH D 53 565 555 HOH HOH . P 4 HOH D 54 566 556 HOH HOH . P 4 HOH D 55 567 558 HOH HOH . P 4 HOH D 56 568 559 HOH HOH . P 4 HOH D 57 569 560 HOH HOH . P 4 HOH D 58 570 561 HOH HOH . P 4 HOH D 59 571 562 HOH HOH . P 4 HOH D 60 572 563 HOH HOH . P 4 HOH D 61 573 564 HOH HOH . P 4 HOH D 62 574 565 HOH HOH . P 4 HOH D 63 575 566 HOH HOH . P 4 HOH D 64 576 567 HOH HOH . P 4 HOH D 65 577 569 HOH HOH . P 4 HOH D 66 578 570 HOH HOH . P 4 HOH D 67 579 571 HOH HOH . P 4 HOH D 68 580 572 HOH HOH . P 4 HOH D 69 581 573 HOH HOH . P 4 HOH D 70 582 574 HOH HOH . P 4 HOH D 71 583 575 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 PMP . . . I 2 71.793 44.077 -44.089 1 11.45 ? N1 PMP 413 C 1 HETATM 2 C C2 PMP . . . I 2 72.809 44.923 -44.372 1 11.56 ? C2 PMP 413 C 1 HETATM 3 C C2A PMP . . . I 2 74.083 44.9 -43.528 1 12.7 ? C2A PMP 413 C 1 HETATM 4 C C3 PMP . . . I 2 72.677 45.81 -45.426 1 21.66 ? C3 PMP 413 C 1 HETATM 5 O O3 PMP . . . I 2 73.718 46.695 -45.737 1 16.01 ? O3 PMP 413 C 1 HETATM 6 C C4 PMP . . . I 2 71.476 45.819 -46.191 1 20.72 ? C4 PMP 413 C 1 HETATM 7 C C4A PMP . . . I 2 71.32 46.791 -47.335 1 24.93 ? C4A PMP 413 C 1 HETATM 8 N N4A PMP . . . I 2 72.537 46.864 -47.963 1 37.42 ? N4A PMP 413 C 1 HETATM 9 C C5 PMP . . . I 2 70.441 44.928 -45.871 1 15.48 ? C5 PMP 413 C 1 HETATM 10 C C6 PMP . . . I 2 70.624 44.07 -44.819 1 18.38 ? C6 PMP 413 C 1 HETATM 11 C C5A PMP . . . I 2 69.087 44.864 -46.636 1 19.2 ? C5A PMP 413 C 1 HETATM 12 O O4P PMP . . . I 2 69.143 45.172 -47.997 1 17.21 ? O4P PMP 413 C 1 HETATM 13 P P PMP . . . I 2 67.84 45.148 -48.886 1 21.16 ? P PMP 413 C 1 HETATM 14 O O1P PMP . . . I 2 67.791 43.735 -49.229 1 10.91 ? O1P PMP 413 C 1 HETATM 15 O O2P PMP . . . I 2 68.235 46.133 -50.041 1 17.83 ? O2P PMP 413 C 1 HETATM 16 O O3P PMP . . . I 2 66.644 45.681 -48.316 1 18.4 ? O3P PMP 413 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #