data_4WYF # _model_server_result.job_id Glm55Bcp8bxK26cuY7jDVg _model_server_result.datetime_utc '2024-12-27 09:27:40' _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 4wyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 4WYF # _exptl.entry_id 4WYF _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 4WYF _cell.length_a 63.086 _cell.length_b 66.092 _cell.length_c 203.194 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WYF _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 _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 E 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 303 A LYS 283 1_555 D C4A PLP . A PLP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 sing covale ? covale2 B NZ LYS 303 B LYS 283 1_555 E C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 sing # _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 4WYF _atom_sites.fract_transf_matrix[1][1] 0.015851 _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] 0.01513 _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] 0.004921 _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 3VX A 1 501 1 3VX DRG . D 3 PLP A 1 502 501 PLP PLP . E 3 PLP B 1 501 501 PLP PLP . F 4 HOH A 1 601 78 HOH HOH . F 4 HOH A 2 602 164 HOH HOH . F 4 HOH A 3 603 28 HOH HOH . F 4 HOH A 4 604 108 HOH HOH . F 4 HOH A 5 605 38 HOH HOH . F 4 HOH A 6 606 60 HOH HOH . F 4 HOH A 7 607 61 HOH HOH . F 4 HOH A 8 608 42 HOH HOH . F 4 HOH A 9 609 93 HOH HOH . F 4 HOH A 10 610 107 HOH HOH . F 4 HOH A 11 611 133 HOH HOH . F 4 HOH A 12 612 175 HOH HOH . F 4 HOH A 13 613 80 HOH HOH . F 4 HOH A 14 614 174 HOH HOH . F 4 HOH A 15 615 30 HOH HOH . F 4 HOH A 16 616 82 HOH HOH . F 4 HOH A 17 617 105 HOH HOH . F 4 HOH A 18 618 101 HOH HOH . F 4 HOH A 19 619 1 HOH HOH . F 4 HOH A 20 620 2 HOH HOH . F 4 HOH A 21 621 3 HOH HOH . F 4 HOH A 22 622 4 HOH HOH . F 4 HOH A 23 623 6 HOH HOH . F 4 HOH A 24 624 10 HOH HOH . F 4 HOH A 25 625 15 HOH HOH . F 4 HOH A 26 626 18 HOH HOH . F 4 HOH A 27 627 20 HOH HOH . F 4 HOH A 28 628 21 HOH HOH . F 4 HOH A 29 629 22 HOH HOH . F 4 HOH A 30 630 23 HOH HOH . F 4 HOH A 31 631 24 HOH HOH . F 4 HOH A 32 632 29 HOH HOH . F 4 HOH A 33 633 31 HOH HOH . F 4 HOH A 34 634 32 HOH HOH . F 4 HOH A 35 635 33 HOH HOH . F 4 HOH A 36 636 34 HOH HOH . F 4 HOH A 37 637 35 HOH HOH . F 4 HOH A 38 638 36 HOH HOH . F 4 HOH A 39 639 37 HOH HOH . F 4 HOH A 40 640 39 HOH HOH . F 4 HOH A 41 641 40 HOH HOH . F 4 HOH A 42 642 41 HOH HOH . F 4 HOH A 43 643 43 HOH HOH . F 4 HOH A 44 644 44 HOH HOH . F 4 HOH A 45 645 45 HOH HOH . F 4 HOH A 46 646 46 HOH HOH . F 4 HOH A 47 647 47 HOH HOH . F 4 HOH A 48 648 49 HOH HOH . F 4 HOH A 49 649 50 HOH HOH . F 4 HOH A 50 650 53 HOH HOH . F 4 HOH A 51 651 54 HOH HOH . F 4 HOH A 52 652 55 HOH HOH . F 4 HOH A 53 653 56 HOH HOH . F 4 HOH A 54 654 57 HOH HOH . F 4 HOH A 55 655 58 HOH HOH . F 4 HOH A 56 656 59 HOH HOH . F 4 HOH A 57 657 62 HOH HOH . F 4 HOH A 58 658 63 HOH HOH . F 4 HOH A 59 659 64 HOH HOH . F 4 HOH A 60 660 66 HOH HOH . F 4 HOH A 61 661 67 HOH HOH . F 4 HOH A 62 662 70 HOH HOH . F 4 HOH A 63 663 71 HOH HOH . F 4 HOH A 64 664 73 HOH HOH . F 4 HOH A 65 665 74 HOH HOH . F 4 HOH A 66 666 79 HOH HOH . F 4 HOH A 67 667 83 HOH HOH . F 4 HOH A 68 668 84 HOH HOH . F 4 HOH A 69 669 85 HOH HOH . F 4 HOH A 70 670 86 HOH HOH . F 4 HOH A 71 671 87 HOH HOH . F 4 HOH A 72 672 88 HOH HOH . F 4 HOH A 73 673 89 HOH HOH . F 4 HOH A 74 674 90 HOH HOH . F 4 HOH A 75 675 91 HOH HOH . F 4 HOH A 76 676 92 HOH HOH . F 4 HOH A 77 677 94 HOH HOH . F 4 HOH A 78 678 95 HOH HOH . F 4 HOH A 79 679 96 HOH HOH . F 4 HOH A 80 680 97 HOH HOH . F 4 HOH A 81 681 99 HOH HOH . F 4 HOH A 82 682 100 HOH HOH . F 4 HOH A 83 683 102 HOH HOH . F 4 HOH A 84 684 103 HOH HOH . F 4 HOH A 85 685 104 HOH HOH . F 4 HOH A 86 686 106 HOH HOH . F 4 HOH A 87 687 109 HOH HOH . F 4 HOH A 88 688 110 HOH HOH . F 4 HOH A 89 689 111 HOH HOH . F 4 HOH A 90 690 112 HOH HOH . F 4 HOH A 91 691 113 HOH HOH . F 4 HOH A 92 692 116 HOH HOH . F 4 HOH A 93 693 117 HOH HOH . F 4 HOH A 94 694 118 HOH HOH . F 4 HOH A 95 695 119 HOH HOH . F 4 HOH A 96 696 120 HOH HOH . F 4 HOH A 97 697 121 HOH HOH . F 4 HOH A 98 698 122 HOH HOH . F 4 HOH A 99 699 123 HOH HOH . F 4 HOH A 100 700 124 HOH HOH . F 4 HOH A 101 701 125 HOH HOH . F 4 HOH A 102 702 126 HOH HOH . F 4 HOH A 103 703 127 HOH HOH . F 4 HOH A 104 704 128 HOH HOH . F 4 HOH A 105 705 129 HOH HOH . F 4 HOH A 106 706 130 HOH HOH . F 4 HOH A 107 707 131 HOH HOH . F 4 HOH A 108 708 132 HOH HOH . F 4 HOH A 109 709 134 HOH HOH . F 4 HOH A 110 710 138 HOH HOH . F 4 HOH A 111 711 148 HOH HOH . F 4 HOH A 112 712 161 HOH HOH . F 4 HOH A 113 713 163 HOH HOH . F 4 HOH A 114 714 165 HOH HOH . F 4 HOH A 115 715 167 HOH HOH . F 4 HOH A 116 716 170 HOH HOH . F 4 HOH A 117 717 172 HOH HOH . F 4 HOH A 118 718 173 HOH HOH . F 4 HOH A 119 719 176 HOH HOH . F 4 HOH A 120 720 183 HOH HOH . F 4 HOH A 121 721 184 HOH HOH . F 4 HOH A 122 722 185 HOH HOH . F 4 HOH A 123 723 191 HOH HOH . G 4 HOH B 1 601 146 HOH HOH . G 4 HOH B 2 602 192 HOH HOH . G 4 HOH B 3 603 195 HOH HOH . G 4 HOH B 4 604 169 HOH HOH . G 4 HOH B 5 605 206 HOH HOH . G 4 HOH B 6 606 81 HOH HOH . G 4 HOH B 7 607 5 HOH HOH . G 4 HOH B 8 608 7 HOH HOH . G 4 HOH B 9 609 8 HOH HOH . G 4 HOH B 10 610 9 HOH HOH . G 4 HOH B 11 611 11 HOH HOH . G 4 HOH B 12 612 12 HOH HOH . G 4 HOH B 13 613 13 HOH HOH . G 4 HOH B 14 614 14 HOH HOH . G 4 HOH B 15 615 16 HOH HOH . G 4 HOH B 16 616 17 HOH HOH . G 4 HOH B 17 617 19 HOH HOH . G 4 HOH B 18 618 25 HOH HOH . G 4 HOH B 19 619 26 HOH HOH . G 4 HOH B 20 620 27 HOH HOH . G 4 HOH B 21 621 48 HOH HOH . G 4 HOH B 22 622 51 HOH HOH . G 4 HOH B 23 623 52 HOH HOH . G 4 HOH B 24 624 65 HOH HOH . G 4 HOH B 25 625 68 HOH HOH . G 4 HOH B 26 626 69 HOH HOH . G 4 HOH B 27 627 72 HOH HOH . G 4 HOH B 28 628 75 HOH HOH . G 4 HOH B 29 629 76 HOH HOH . G 4 HOH B 30 630 77 HOH HOH . G 4 HOH B 31 631 114 HOH HOH . G 4 HOH B 32 632 115 HOH HOH . G 4 HOH B 33 633 135 HOH HOH . G 4 HOH B 34 634 136 HOH HOH . G 4 HOH B 35 635 137 HOH HOH . G 4 HOH B 36 636 139 HOH HOH . G 4 HOH B 37 637 140 HOH HOH . G 4 HOH B 38 638 141 HOH HOH . G 4 HOH B 39 639 142 HOH HOH . G 4 HOH B 40 640 143 HOH HOH . G 4 HOH B 41 641 144 HOH HOH . G 4 HOH B 42 642 145 HOH HOH . G 4 HOH B 43 643 147 HOH HOH . G 4 HOH B 44 644 149 HOH HOH . G 4 HOH B 45 645 150 HOH HOH . G 4 HOH B 46 646 151 HOH HOH . G 4 HOH B 47 647 152 HOH HOH . G 4 HOH B 48 648 153 HOH HOH . G 4 HOH B 49 649 154 HOH HOH . G 4 HOH B 50 650 155 HOH HOH . G 4 HOH B 51 651 156 HOH HOH . G 4 HOH B 52 652 157 HOH HOH . G 4 HOH B 53 653 158 HOH HOH . G 4 HOH B 54 654 159 HOH HOH . G 4 HOH B 55 655 160 HOH HOH . G 4 HOH B 56 656 162 HOH HOH . G 4 HOH B 57 657 166 HOH HOH . G 4 HOH B 58 658 168 HOH HOH . G 4 HOH B 59 659 171 HOH HOH . G 4 HOH B 60 660 177 HOH HOH . G 4 HOH B 61 661 178 HOH HOH . G 4 HOH B 62 662 179 HOH HOH . G 4 HOH B 63 663 180 HOH HOH . G 4 HOH B 64 664 181 HOH HOH . G 4 HOH B 65 665 182 HOH HOH . G 4 HOH B 66 666 186 HOH HOH . G 4 HOH B 67 667 187 HOH HOH . G 4 HOH B 68 668 188 HOH HOH . G 4 HOH B 69 669 189 HOH HOH . G 4 HOH B 70 670 190 HOH HOH . G 4 HOH B 71 671 193 HOH HOH . G 4 HOH B 72 672 194 HOH HOH . G 4 HOH B 73 673 196 HOH HOH . G 4 HOH B 74 674 197 HOH HOH . G 4 HOH B 75 675 198 HOH HOH . G 4 HOH B 76 676 199 HOH HOH . G 4 HOH B 77 677 200 HOH HOH . G 4 HOH B 78 678 201 HOH HOH . G 4 HOH B 79 679 202 HOH HOH . G 4 HOH B 80 680 203 HOH HOH . G 4 HOH B 81 681 204 HOH HOH . G 4 HOH B 82 682 205 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 . . . E 3 6.689 42.36 -28.874 1 9.23 ? N1 PLP 501 B 1 HETATM 2 C C2 PLP . . . E 3 7.96 42.821 -28.718 1 9.47 ? C2 PLP 501 B 1 HETATM 3 C C2A PLP . . . E 3 8.278 44.292 -28.775 1 9.3 ? C2A PLP 501 B 1 HETATM 4 C C3 PLP . . . E 3 9.064 41.853 -28.509 1 9.52 ? C3 PLP 501 B 1 HETATM 5 O O3 PLP . . . E 3 10.349 42.264 -28.347 1 9.8 ? O3 PLP 501 B 1 HETATM 6 C C4 PLP . . . E 3 8.711 40.418 -28.455 1 9.48 ? C4 PLP 501 B 1 HETATM 7 C C4A PLP . . . E 3 9.751 39.365 -28.23 1 9.49 ? C4A PLP 501 B 1 HETATM 8 C C5 PLP . . . E 3 7.295 40.041 -28.645 1 9.29 ? C5 PLP 501 B 1 HETATM 9 C C6 PLP . . . E 3 6.366 41.058 -28.843 1 9.16 ? C6 PLP 501 B 1 HETATM 10 C C5A PLP . . . E 3 6.894 38.58 -28.624 1 9.1 ? C5A PLP 501 B 1 HETATM 11 O O4P PLP . . . E 3 7.304 37.962 -27.4 1 9.17 ? O4P PLP 501 B 1 HETATM 12 P P PLP . . . E 3 7.43 36.356 -27.303 1 9.08 ? P PLP 501 B 1 HETATM 13 O O1P PLP . . . E 3 8.656 36.017 -28.088 1 9.31 ? O1P PLP 501 B 1 HETATM 14 O O2P PLP . . . E 3 6.154 35.829 -27.909 1 9.16 ? O2P PLP 501 B 1 HETATM 15 O O3P PLP . . . E 3 7.531 36.062 -25.825 1 9.46 ? O3P PLP 501 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #