data_1YJS # _model_server_result.job_id zE6RzT77uQfd16ZL1ZbxxA _model_server_result.datetime_utc '2024-12-01 12:39:06' _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 1yjs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 1YJS # _exptl.entry_id 1YJS _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 1YJS _cell.length_a 61.365 _cell.length_b 106.287 _cell.length_c 56.981 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YJS _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,PQS _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 _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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C4A _struct_conn.ptnr1_label_comp_id PLP _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id PLP _struct_conn.ptnr1_auth_seq_id 501 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id GLY _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id GLY _struct_conn.ptnr2_auth_seq_id 601 _struct_conn.ptnr2_symmetry 1_555 _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 1.411 _struct_conn.pdbx_value_order ? # _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 1YJS _atom_sites.fract_transf_matrix[1][1] 0.016296 _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] 0.009408 _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] 0.01755 _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 1 501 501 PLP PLP . C 3 GLY A 1 601 601 GLY GLY . D 4 HOH A 1 602 1 HOH HOH . D 4 HOH A 2 603 2 HOH HOH . D 4 HOH A 3 604 3 HOH HOH . D 4 HOH A 4 605 4 HOH HOH . D 4 HOH A 5 606 5 HOH HOH . D 4 HOH A 6 607 6 HOH HOH . D 4 HOH A 7 608 7 HOH HOH . D 4 HOH A 8 609 8 HOH HOH . D 4 HOH A 9 610 9 HOH HOH . D 4 HOH A 10 611 10 HOH HOH . D 4 HOH A 11 612 11 HOH HOH . D 4 HOH A 12 613 12 HOH HOH . D 4 HOH A 13 614 13 HOH HOH . D 4 HOH A 14 615 14 HOH HOH . D 4 HOH A 15 616 15 HOH HOH . D 4 HOH A 16 617 16 HOH HOH . D 4 HOH A 17 618 17 HOH HOH . D 4 HOH A 18 619 18 HOH HOH . D 4 HOH A 19 620 19 HOH HOH . D 4 HOH A 20 621 20 HOH HOH . D 4 HOH A 21 622 21 HOH HOH . D 4 HOH A 22 623 22 HOH HOH . D 4 HOH A 23 624 23 HOH HOH . D 4 HOH A 24 625 24 HOH HOH . D 4 HOH A 25 626 25 HOH HOH . D 4 HOH A 26 627 26 HOH HOH . D 4 HOH A 27 628 27 HOH HOH . D 4 HOH A 28 629 28 HOH HOH . D 4 HOH A 29 630 29 HOH HOH . D 4 HOH A 30 631 30 HOH HOH . D 4 HOH A 31 632 31 HOH HOH . D 4 HOH A 32 633 32 HOH HOH . D 4 HOH A 33 634 33 HOH HOH . D 4 HOH A 34 635 34 HOH HOH . D 4 HOH A 35 636 35 HOH HOH . D 4 HOH A 36 637 36 HOH HOH . D 4 HOH A 37 638 37 HOH HOH . D 4 HOH A 38 639 38 HOH HOH . D 4 HOH A 39 640 39 HOH HOH . D 4 HOH A 40 641 40 HOH HOH . D 4 HOH A 41 642 41 HOH HOH . D 4 HOH A 42 643 42 HOH HOH . D 4 HOH A 43 644 43 HOH HOH . D 4 HOH A 44 645 44 HOH HOH . D 4 HOH A 45 646 45 HOH HOH . D 4 HOH A 46 647 46 HOH HOH . D 4 HOH A 47 648 47 HOH HOH . D 4 HOH A 48 649 48 HOH HOH . D 4 HOH A 49 650 49 HOH HOH . D 4 HOH A 50 651 50 HOH HOH . D 4 HOH A 51 652 51 HOH HOH . D 4 HOH A 52 653 52 HOH HOH . D 4 HOH A 53 654 53 HOH HOH . D 4 HOH A 54 655 54 HOH HOH . D 4 HOH A 55 656 55 HOH HOH . D 4 HOH A 56 657 56 HOH HOH . D 4 HOH A 57 658 57 HOH HOH . D 4 HOH A 58 659 58 HOH HOH . D 4 HOH A 59 660 59 HOH HOH . D 4 HOH A 60 661 60 HOH HOH . D 4 HOH A 61 662 61 HOH HOH . D 4 HOH A 62 663 62 HOH HOH . D 4 HOH A 63 664 63 HOH HOH . D 4 HOH A 64 665 64 HOH HOH . D 4 HOH A 65 666 65 HOH HOH . D 4 HOH A 66 667 66 HOH HOH . D 4 HOH A 67 668 67 HOH HOH . D 4 HOH A 68 669 68 HOH HOH . D 4 HOH A 69 670 69 HOH HOH . D 4 HOH A 70 671 70 HOH HOH . D 4 HOH A 71 672 71 HOH HOH . D 4 HOH A 72 673 72 HOH HOH . D 4 HOH A 73 674 73 HOH HOH . D 4 HOH A 74 675 74 HOH HOH . D 4 HOH A 75 676 75 HOH HOH . D 4 HOH A 76 677 76 HOH HOH . D 4 HOH A 77 678 77 HOH HOH . D 4 HOH A 78 679 78 HOH HOH . D 4 HOH A 79 680 79 HOH HOH . D 4 HOH A 80 681 80 HOH HOH . D 4 HOH A 81 682 81 HOH HOH . D 4 HOH A 82 683 82 HOH HOH . D 4 HOH A 83 684 83 HOH HOH . D 4 HOH A 84 685 84 HOH HOH . D 4 HOH A 85 686 85 HOH HOH . D 4 HOH A 86 687 86 HOH HOH . D 4 HOH A 87 688 87 HOH HOH . D 4 HOH A 88 689 88 HOH HOH . D 4 HOH A 89 690 89 HOH HOH . D 4 HOH A 90 691 90 HOH HOH . D 4 HOH A 91 692 91 HOH HOH . D 4 HOH A 92 693 92 HOH HOH . D 4 HOH A 93 694 93 HOH HOH . D 4 HOH A 94 695 94 HOH HOH . D 4 HOH A 95 696 95 HOH HOH . D 4 HOH A 96 697 96 HOH HOH . D 4 HOH A 97 698 97 HOH HOH . D 4 HOH A 98 699 98 HOH HOH . D 4 HOH A 99 700 99 HOH HOH . D 4 HOH A 100 701 100 HOH HOH . D 4 HOH A 101 702 101 HOH HOH . D 4 HOH A 102 703 102 HOH HOH . D 4 HOH A 103 704 103 HOH HOH . D 4 HOH A 104 705 104 HOH HOH . D 4 HOH A 105 706 105 HOH HOH . D 4 HOH A 106 707 106 HOH HOH . D 4 HOH A 107 708 107 HOH HOH . D 4 HOH A 108 709 108 HOH HOH . D 4 HOH A 109 710 109 HOH HOH . D 4 HOH A 110 711 110 HOH HOH . D 4 HOH A 111 712 111 HOH HOH . D 4 HOH A 112 713 112 HOH HOH . D 4 HOH A 113 714 113 HOH HOH . D 4 HOH A 114 715 114 HOH HOH . D 4 HOH A 115 716 115 HOH HOH . D 4 HOH A 116 717 116 HOH HOH . D 4 HOH A 117 718 117 HOH HOH . D 4 HOH A 118 719 118 HOH HOH . D 4 HOH A 119 720 119 HOH HOH . D 4 HOH A 120 721 120 HOH HOH . D 4 HOH A 121 722 121 HOH HOH . D 4 HOH A 122 723 122 HOH HOH . D 4 HOH A 123 724 123 HOH HOH . D 4 HOH A 124 725 124 HOH HOH . D 4 HOH A 125 726 125 HOH HOH . D 4 HOH A 126 727 126 HOH HOH . D 4 HOH A 127 728 127 HOH HOH . D 4 HOH A 128 729 128 HOH HOH . D 4 HOH A 129 730 129 HOH HOH . D 4 HOH A 130 731 130 HOH HOH . D 4 HOH A 131 732 131 HOH HOH . D 4 HOH A 132 733 132 HOH HOH . D 4 HOH A 133 734 133 HOH HOH . D 4 HOH A 134 735 134 HOH HOH . D 4 HOH A 135 736 135 HOH HOH . D 4 HOH A 136 737 136 HOH HOH . D 4 HOH A 137 738 137 HOH HOH . D 4 HOH A 138 739 138 HOH HOH . D 4 HOH A 139 740 139 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 9.717 9.226 22.386 1 14.54 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . B 2 10.154 10.443 21.931 1 14.73 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . B 2 11.503 10.84 22.407 1 12.73 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . B 2 9.273 11.166 21.051 1 14.51 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . B 2 9.683 12.322 20.53 1 16.92 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . B 2 8 10.593 20.724 1 13.88 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . B 2 7.075 11.312 19.862 1 13.17 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . B 2 7.598 9.346 21.258 1 13.85 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . B 2 8.5 8.676 22.108 1 13.23 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . B 2 6.289 8.651 21.099 1 11.61 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . B 2 6.192 8.061 19.789 1 11.53 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . B 2 4.822 7.624 19.163 1 12.87 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . B 2 4.053 6.966 20.24 1 12.01 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . B 2 4.178 9.022 18.741 1 13.41 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . B 2 5.131 6.917 17.91 1 14.79 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 15 #