data_8SBG # _model_server_result.job_id 9zGPieLlZxq4HXtXUTJibg _model_server_result.datetime_utc '2025-07-15 10:21:07' _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 8sbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8SBG # _exptl.entry_id 8SBG _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 120 _cell.entry_id 8SBG _cell.length_a 100.836 _cell.length_b 100.836 _cell.length_c 228.406 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall 'P 64 2 (x,y,z+1/6)' _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 4_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -50.418 -87.326538 0 3 '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 76.135333 4 'crystal symmetry operation' 10_445 -y-1,-x-1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -50.418 -87.326538 76.135333 # _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 A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 278 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 259 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 501 _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 1.435 _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 8SBG _atom_sites.fract_transf_matrix[1][1] 0.009917 _atom_sites.fract_transf_matrix[1][2] 0.005726 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011451 _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] 0.004378 _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 HOH A 1 601 24 HOH HOH . C 3 HOH A 2 602 150 HOH HOH . C 3 HOH A 3 603 125 HOH HOH . C 3 HOH A 4 604 203 HOH HOH . C 3 HOH A 5 605 106 HOH HOH . C 3 HOH A 6 606 29 HOH HOH . C 3 HOH A 7 607 120 HOH HOH . C 3 HOH A 8 608 57 HOH HOH . C 3 HOH A 9 609 169 HOH HOH . C 3 HOH A 10 610 41 HOH HOH . C 3 HOH A 11 611 121 HOH HOH . C 3 HOH A 12 612 147 HOH HOH . C 3 HOH A 13 613 172 HOH HOH . C 3 HOH A 14 614 39 HOH HOH . C 3 HOH A 15 615 78 HOH HOH . C 3 HOH A 16 616 59 HOH HOH . C 3 HOH A 17 617 100 HOH HOH . C 3 HOH A 18 618 107 HOH HOH . C 3 HOH A 19 619 111 HOH HOH . C 3 HOH A 20 620 31 HOH HOH . C 3 HOH A 21 621 81 HOH HOH . C 3 HOH A 22 622 122 HOH HOH . C 3 HOH A 23 623 44 HOH HOH . C 3 HOH A 24 624 33 HOH HOH . C 3 HOH A 25 625 104 HOH HOH . C 3 HOH A 26 626 35 HOH HOH . C 3 HOH A 27 627 175 HOH HOH . C 3 HOH A 28 628 93 HOH HOH . C 3 HOH A 29 629 48 HOH HOH . C 3 HOH A 30 630 69 HOH HOH . C 3 HOH A 31 631 49 HOH HOH . C 3 HOH A 32 632 68 HOH HOH . C 3 HOH A 33 633 23 HOH HOH . C 3 HOH A 34 634 7 HOH HOH . C 3 HOH A 35 635 28 HOH HOH . C 3 HOH A 36 636 71 HOH HOH . C 3 HOH A 37 637 1 HOH HOH . C 3 HOH A 38 638 3 HOH HOH . C 3 HOH A 39 639 94 HOH HOH . C 3 HOH A 40 640 126 HOH HOH . C 3 HOH A 41 641 70 HOH HOH . C 3 HOH A 42 642 132 HOH HOH . C 3 HOH A 43 643 5 HOH HOH . C 3 HOH A 44 644 32 HOH HOH . C 3 HOH A 45 645 12 HOH HOH . C 3 HOH A 46 646 124 HOH HOH . C 3 HOH A 47 647 21 HOH HOH . C 3 HOH A 48 648 128 HOH HOH . C 3 HOH A 49 649 77 HOH HOH . C 3 HOH A 50 650 19 HOH HOH . C 3 HOH A 51 651 137 HOH HOH . C 3 HOH A 52 652 2 HOH HOH . C 3 HOH A 53 653 60 HOH HOH . C 3 HOH A 54 654 73 HOH HOH . C 3 HOH A 55 655 56 HOH HOH . C 3 HOH A 56 656 6 HOH HOH . C 3 HOH A 57 657 99 HOH HOH . C 3 HOH A 58 658 14 HOH HOH . C 3 HOH A 59 659 15 HOH HOH . C 3 HOH A 60 660 129 HOH HOH . C 3 HOH A 61 661 4 HOH HOH . C 3 HOH A 62 662 34 HOH HOH . C 3 HOH A 63 663 22 HOH HOH . C 3 HOH A 64 664 10 HOH HOH . C 3 HOH A 65 665 50 HOH HOH . C 3 HOH A 66 666 38 HOH HOH . C 3 HOH A 67 667 11 HOH HOH . C 3 HOH A 68 668 176 HOH HOH . C 3 HOH A 69 669 55 HOH HOH . C 3 HOH A 70 670 25 HOH HOH . C 3 HOH A 71 671 52 HOH HOH . C 3 HOH A 72 672 181 HOH HOH . C 3 HOH A 73 673 165 HOH HOH . C 3 HOH A 74 674 36 HOH HOH . C 3 HOH A 75 675 74 HOH HOH . C 3 HOH A 76 676 136 HOH HOH . C 3 HOH A 77 677 83 HOH HOH . C 3 HOH A 78 678 133 HOH HOH . C 3 HOH A 79 679 18 HOH HOH . C 3 HOH A 80 680 8 HOH HOH . C 3 HOH A 81 681 87 HOH HOH . C 3 HOH A 82 682 65 HOH HOH . C 3 HOH A 83 683 54 HOH HOH . C 3 HOH A 84 684 17 HOH HOH . C 3 HOH A 85 685 103 HOH HOH . C 3 HOH A 86 686 30 HOH HOH . C 3 HOH A 87 687 45 HOH HOH . C 3 HOH A 88 688 212 HOH HOH . C 3 HOH A 89 689 76 HOH HOH . C 3 HOH A 90 690 42 HOH HOH . C 3 HOH A 91 691 58 HOH HOH . C 3 HOH A 92 692 64 HOH HOH . C 3 HOH A 93 693 138 HOH HOH . C 3 HOH A 94 694 182 HOH HOH . C 3 HOH A 95 695 139 HOH HOH . C 3 HOH A 96 696 170 HOH HOH . C 3 HOH A 97 697 40 HOH HOH . C 3 HOH A 98 698 191 HOH HOH . C 3 HOH A 99 699 207 HOH HOH . C 3 HOH A 100 700 46 HOH HOH . C 3 HOH A 101 701 88 HOH HOH . C 3 HOH A 102 702 102 HOH HOH . C 3 HOH A 103 703 84 HOH HOH . C 3 HOH A 104 704 20 HOH HOH . C 3 HOH A 105 705 148 HOH HOH . C 3 HOH A 106 706 173 HOH HOH . C 3 HOH A 107 707 51 HOH HOH . C 3 HOH A 108 708 26 HOH HOH . C 3 HOH A 109 709 72 HOH HOH . C 3 HOH A 110 710 159 HOH HOH . C 3 HOH A 111 711 123 HOH HOH . C 3 HOH A 112 712 16 HOH HOH . C 3 HOH A 113 713 53 HOH HOH . C 3 HOH A 114 714 155 HOH HOH . C 3 HOH A 115 715 210 HOH HOH . C 3 HOH A 116 716 96 HOH HOH . C 3 HOH A 117 717 9 HOH HOH . C 3 HOH A 118 718 43 HOH HOH . C 3 HOH A 119 719 142 HOH HOH . C 3 HOH A 120 720 92 HOH HOH . C 3 HOH A 121 721 47 HOH HOH . C 3 HOH A 122 722 79 HOH HOH . C 3 HOH A 123 723 105 HOH HOH . C 3 HOH A 124 724 85 HOH HOH . C 3 HOH A 125 725 188 HOH HOH . C 3 HOH A 126 726 67 HOH HOH . C 3 HOH A 127 727 110 HOH HOH . C 3 HOH A 128 728 180 HOH HOH . C 3 HOH A 129 729 152 HOH HOH . C 3 HOH A 130 730 149 HOH HOH . C 3 HOH A 131 731 101 HOH HOH . C 3 HOH A 132 732 185 HOH HOH . C 3 HOH A 133 733 86 HOH HOH . C 3 HOH A 134 734 134 HOH HOH . C 3 HOH A 135 735 144 HOH HOH . C 3 HOH A 136 736 197 HOH HOH . C 3 HOH A 137 737 62 HOH HOH . C 3 HOH A 138 738 178 HOH HOH . C 3 HOH A 139 739 98 HOH HOH . C 3 HOH A 140 740 75 HOH HOH . C 3 HOH A 141 741 114 HOH HOH . C 3 HOH A 142 742 127 HOH HOH . C 3 HOH A 143 743 195 HOH HOH . C 3 HOH A 144 744 184 HOH HOH . C 3 HOH A 145 745 117 HOH HOH . C 3 HOH A 146 746 89 HOH HOH . C 3 HOH A 147 747 95 HOH HOH . C 3 HOH A 148 748 177 HOH HOH . C 3 HOH A 149 749 151 HOH HOH . C 3 HOH A 150 750 135 HOH HOH . C 3 HOH A 151 751 160 HOH HOH . C 3 HOH A 152 752 141 HOH HOH . C 3 HOH A 153 753 205 HOH HOH . C 3 HOH A 154 754 216 HOH HOH . C 3 HOH A 155 755 115 HOH HOH . C 3 HOH A 156 756 162 HOH HOH . C 3 HOH A 157 757 174 HOH HOH . C 3 HOH A 158 758 146 HOH HOH . C 3 HOH A 159 759 37 HOH HOH . C 3 HOH A 160 760 91 HOH HOH . C 3 HOH A 161 761 116 HOH HOH . C 3 HOH A 162 762 153 HOH HOH . C 3 HOH A 163 763 215 HOH HOH . C 3 HOH A 164 764 82 HOH HOH . C 3 HOH A 165 765 97 HOH HOH . C 3 HOH A 166 766 196 HOH HOH . C 3 HOH A 167 767 130 HOH HOH . C 3 HOH A 168 768 157 HOH HOH . C 3 HOH A 169 769 171 HOH HOH . C 3 HOH A 170 770 164 HOH HOH . C 3 HOH A 171 771 220 HOH HOH . C 3 HOH A 172 772 166 HOH HOH . C 3 HOH A 173 773 194 HOH HOH . C 3 HOH A 174 774 131 HOH HOH . C 3 HOH A 175 775 209 HOH HOH . C 3 HOH A 176 776 183 HOH HOH . C 3 HOH A 177 777 179 HOH HOH . C 3 HOH A 178 778 208 HOH HOH . C 3 HOH A 179 779 211 HOH HOH . C 3 HOH A 180 780 158 HOH HOH . C 3 HOH A 181 781 168 HOH HOH . C 3 HOH A 182 782 61 HOH HOH . C 3 HOH A 183 783 192 HOH HOH . C 3 HOH A 184 784 119 HOH HOH . C 3 HOH A 185 785 140 HOH HOH . C 3 HOH A 186 786 213 HOH HOH . C 3 HOH A 187 787 199 HOH HOH . C 3 HOH A 188 788 118 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 -7.525 -23.81 23.948 1 43.01 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . B 2 -8.241 -24.297 22.88 1 42.06 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . B 2 -7.505 -24.637 21.623 1 41.85 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . B 2 -9.618 -24.457 22.958 1 44.45 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . B 2 -10.295 -24.938 21.861 1 43.7 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . B 2 -10.302 -24.136 24.14 1 43.82 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . B 2 -11.629 -24.816 24.395 1 42.83 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . B 2 -9.551 -23.637 25.217 1 44.98 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . B 2 -8.174 -23.484 25.109 1 45.64 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . B 2 -10.17 -23.218 26.541 1 43.64 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . B 2 -10.737 -24.286 27.239 1 42.79 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . B 2 -12.06 -24.078 28.098 1 38.43 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . B 2 -13.267 -23.78 27.233 1 35.48 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . B 2 -12.238 -25.384 28.809 1 38.34 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . B 2 -11.857 -22.959 29.095 1 38 ? O3P PLP 501 A 1 HETATM 16 H H2A1 PLP . . . B 2 -8.166 -24.499 20.767 1 50.31 ? H2A1 PLP 501 A 1 HETATM 17 H H2A2 PLP . . . B 2 -7.176 -25.675 21.664 1 50.31 ? H2A2 PLP 501 A 1 HETATM 18 H H2A3 PLP . . . B 2 -6.638 -23.985 21.521 1 50.31 ? H2A3 PLP 501 A 1 HETATM 19 H HO3 PLP . . . B 2 -11.211 -24.591 21.866 1 52.54 ? HO3 PLP 501 A 1 HETATM 20 H H4A PLP . . . B 2 -12.556 -24.306 24.129 1 51.48 ? H4A PLP 501 A 1 HETATM 21 H H6 PLP . . . B 2 -7.605 -23.1 25.957 1 54.87 ? H6 PLP 501 A 1 HETATM 22 H H5A1 PLP . . . B 2 -10.94 -22.471 26.35 1 52.46 ? H5A1 PLP 501 A 1 HETATM 23 H H5A2 PLP . . . B 2 -9.402 -22.757 27.161 1 52.46 ? H5A2 PLP 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #