data_1DGD # _model_server_result.job_id 1HqqW_0X5j1X80SnE-41oQ _model_server_result.datetime_utc '2024-11-24 09:03:23' _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 1dgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":437}' # _entry.id 1DGD # _exptl.entry_id 1DGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _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 120 _cell.entry_id 1DGD _cell.length_a 152.7 _cell.length_b 152.7 _cell.length_c 86.6 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.866667 3 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.35 132.242079 28.866667 4 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.35 132.242079 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 271 A LYS 272 1_555 D C4A PLP . A PLP 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? metalc ? metalc1 B NA NA . A NA 435 1_555 A O ALA 94 A ALA 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 B NA NA . A NA 435 1_555 A O LEU 101 A LEU 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc3 B NA NA . A NA 435 1_555 F O HOH . A HOH 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc4 B NA NA . A NA 435 1_555 A O PRO 98 A PRO 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc5 B NA NA . A NA 435 1_555 A O THR 97 A THR 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc6 C LI LI . A LI 436 1_555 F O HOH . A HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc7 C LI LI . A LI 436 1_555 A O LEU 77 A LEU 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc8 C LI LI . A LI 436 1_555 F O HOH . A HOH 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc9 C LI LI . A LI 436 1_555 A OD1 ASP 306 A ASP 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc10 A OG1 THR 97 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? # _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' # _atom_sites.entry_id 1DGD _atom_sites.fract_transf_matrix[1][1] 0.006549 _atom_sites.fract_transf_matrix[1][2] 0.003781 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007562 _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] 0.011547 _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 NA A 1 435 435 NA NA . C 3 LI A 1 436 436 LI LI . D 4 PLP A 1 437 272 PLP PLP . E 5 MES A 1 434 434 MES MES . F 6 HOH A 1 501 501 HOH HOH . F 6 HOH A 2 502 502 HOH HOH . F 6 HOH A 3 503 503 HOH HOH . F 6 HOH A 4 504 504 HOH HOH . F 6 HOH A 5 505 505 HOH HOH . F 6 HOH A 6 506 506 HOH HOH . F 6 HOH A 7 507 507 HOH HOH . F 6 HOH A 8 508 508 HOH HOH . F 6 HOH A 9 509 509 HOH HOH . F 6 HOH A 10 510 510 HOH HOH . F 6 HOH A 11 511 511 HOH HOH . F 6 HOH A 12 512 512 HOH HOH . F 6 HOH A 13 513 513 HOH HOH . F 6 HOH A 14 514 514 HOH HOH . F 6 HOH A 15 515 515 HOH HOH . F 6 HOH A 16 516 516 HOH HOH . F 6 HOH A 17 517 517 HOH HOH . F 6 HOH A 18 518 518 HOH HOH . F 6 HOH A 19 519 519 HOH HOH . F 6 HOH A 20 520 520 HOH HOH . F 6 HOH A 21 521 521 HOH HOH . F 6 HOH A 22 522 522 HOH HOH . F 6 HOH A 23 523 523 HOH HOH . F 6 HOH A 24 524 524 HOH HOH . F 6 HOH A 25 525 525 HOH HOH . F 6 HOH A 26 526 526 HOH HOH . F 6 HOH A 27 527 527 HOH HOH . F 6 HOH A 28 528 528 HOH HOH . F 6 HOH A 29 529 529 HOH HOH . F 6 HOH A 30 530 530 HOH HOH . F 6 HOH A 31 531 531 HOH HOH . F 6 HOH A 32 532 532 HOH HOH . F 6 HOH A 33 533 533 HOH HOH . F 6 HOH A 34 534 534 HOH HOH . F 6 HOH A 35 535 535 HOH HOH . F 6 HOH A 36 536 536 HOH HOH . F 6 HOH A 37 537 537 HOH HOH . F 6 HOH A 38 538 538 HOH HOH . F 6 HOH A 39 539 539 HOH HOH . F 6 HOH A 40 540 540 HOH HOH . F 6 HOH A 41 541 541 HOH HOH . F 6 HOH A 42 542 542 HOH HOH . F 6 HOH A 43 543 543 HOH HOH . F 6 HOH A 44 544 544 HOH HOH . F 6 HOH A 45 545 545 HOH HOH . F 6 HOH A 46 546 546 HOH HOH . F 6 HOH A 47 547 547 HOH HOH . F 6 HOH A 48 548 548 HOH HOH . F 6 HOH A 49 549 549 HOH HOH . F 6 HOH A 50 550 550 HOH HOH . F 6 HOH A 51 551 551 HOH HOH . F 6 HOH A 52 552 552 HOH HOH . F 6 HOH A 53 553 553 HOH HOH . F 6 HOH A 54 554 554 HOH HOH . F 6 HOH A 55 555 555 HOH HOH . F 6 HOH A 56 556 556 HOH HOH . F 6 HOH A 57 557 557 HOH HOH . F 6 HOH A 58 558 558 HOH HOH . F 6 HOH A 59 559 559 HOH HOH . F 6 HOH A 60 560 560 HOH HOH . F 6 HOH A 61 561 561 HOH HOH . F 6 HOH A 62 562 562 HOH HOH . F 6 HOH A 63 563 563 HOH HOH . F 6 HOH A 64 564 564 HOH HOH . F 6 HOH A 65 565 565 HOH HOH . F 6 HOH A 66 566 566 HOH HOH . F 6 HOH A 67 567 567 HOH HOH . F 6 HOH A 68 568 568 HOH HOH . F 6 HOH A 69 569 569 HOH HOH . F 6 HOH A 70 570 570 HOH HOH . F 6 HOH A 71 571 571 HOH HOH . F 6 HOH A 72 572 572 HOH HOH . F 6 HOH A 73 573 573 HOH HOH . F 6 HOH A 74 574 574 HOH HOH . F 6 HOH A 75 575 575 HOH HOH . F 6 HOH A 76 576 576 HOH HOH . F 6 HOH A 77 577 577 HOH HOH . F 6 HOH A 78 578 578 HOH HOH . F 6 HOH A 79 579 579 HOH HOH . F 6 HOH A 80 580 580 HOH HOH . F 6 HOH A 81 581 581 HOH HOH . F 6 HOH A 82 582 582 HOH HOH . F 6 HOH A 83 583 583 HOH HOH . F 6 HOH A 84 584 584 HOH HOH . F 6 HOH A 85 585 585 HOH HOH . F 6 HOH A 86 586 586 HOH HOH . F 6 HOH A 87 587 587 HOH HOH . F 6 HOH A 88 588 588 HOH HOH . F 6 HOH A 89 589 589 HOH HOH . F 6 HOH A 90 590 590 HOH HOH . F 6 HOH A 91 591 591 HOH HOH . F 6 HOH A 92 592 592 HOH HOH . F 6 HOH A 93 593 593 HOH HOH . F 6 HOH A 94 594 594 HOH HOH . F 6 HOH A 95 595 595 HOH HOH . F 6 HOH A 96 596 596 HOH HOH . F 6 HOH A 97 597 597 HOH HOH . F 6 HOH A 98 598 598 HOH HOH . F 6 HOH A 99 599 599 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 4 17.878 53.523 13.669 1 28.65 ? N1 PLP 437 A 1 HETATM 2 C C2 PLP . . . D 4 16.648 53.55 14.255 1 27.18 ? C2 PLP 437 A 1 HETATM 3 C C2A PLP . . . D 4 15.664 54.596 13.804 1 27.15 ? C2A PLP 437 A 1 HETATM 4 C C3 PLP . . . D 4 16.452 52.601 15.25 1 26.47 ? C3 PLP 437 A 1 HETATM 5 O O3 PLP . . . D 4 15.231 52.639 15.816 1 27.96 ? O3 PLP 437 A 1 HETATM 6 C C4 PLP . . . D 4 17.41 51.694 15.577 1 26.31 ? C4 PLP 437 A 1 HETATM 7 C C4A PLP . . . D 4 17.124 50.701 16.575 1 27.26 ? C4A PLP 437 A 1 HETATM 8 C C5 PLP . . . D 4 18.648 51.732 14.887 1 27.22 ? C5 PLP 437 A 1 HETATM 9 C C6 PLP . . . D 4 18.876 52.674 13.933 1 28.51 ? C6 PLP 437 A 1 HETATM 10 C C5A PLP . . . D 4 19.789 50.76 15.226 1 28.51 ? C5A PLP 437 A 1 HETATM 11 O O4P PLP . . . D 4 19.503 49.384 15.294 1 30.14 ? O4P PLP 437 A 1 HETATM 12 P P PLP . . . D 4 20.396 48.43 16.224 1 30.03 ? P PLP 437 A 1 HETATM 13 O O1P PLP . . . D 4 20.028 47.009 16.018 1 28.18 ? O1P PLP 437 A 1 HETATM 14 O O2P PLP . . . D 4 20.113 48.886 17.586 1 30.32 ? O2P PLP 437 A 1 HETATM 15 O O3P PLP . . . D 4 21.905 48.659 15.895 1 29.66 ? O3P PLP 437 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #