data_3FDD # _model_server_result.job_id EL829eCqabCzJvgFIbuL1w _model_server_result.datetime_utc '2025-04-06 01:28:52' _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 3fdd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":534}' # _entry.id 3FDD # _exptl.entry_id 3FDD _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 3FDD _cell.length_a 150.453 _cell.length_b 150.453 _cell.length_c 150.453 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3FDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12 # 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 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 6 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 7 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 10 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 12 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 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 A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 315 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 315 _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 534 _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 1.542 _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 266 n y N1 C6 PLP sing 267 n y C2 C2A PLP sing 268 n n C2 C3 PLP sing 269 n y C2A H2A1 PLP sing 270 n n C2A H2A2 PLP sing 271 n n C2A H2A3 PLP sing 272 n n C3 O3 PLP sing 273 n n C3 C4 PLP doub 274 n y O3 HO3 PLP sing 275 n n C4 C4A PLP sing 276 n n C4 C5 PLP sing 277 n y C4A O4A PLP doub 278 n n C4A H4A PLP sing 279 n n C5 C6 PLP doub 280 n y C5 C5A PLP sing 281 n n C6 H6 PLP sing 282 n n C5A O4P PLP sing 283 n n C5A H5A1 PLP sing 284 n n C5A H5A2 PLP sing 285 n n O4P P PLP sing 286 n n P O1P PLP doub 287 n n P O2P PLP sing 288 n n P O3P PLP sing 289 n n O2P HOP2 PLP sing 290 n n O3P HOP3 PLP sing 291 n n # _atom_sites.entry_id 3FDD _atom_sites.fract_transf_matrix[1][1] 0.006647 _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] 0.006647 _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] 0.006647 _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 1 534 534 PLP PLP . C 3 ACT A 1 535 535 ACT ACT . D 4 CL A 1 536 536 CL CL . E 5 HOH A 1 537 537 HOH HOH . E 5 HOH A 2 538 538 HOH HOH . E 5 HOH A 3 539 539 HOH HOH . E 5 HOH A 4 540 540 HOH HOH . E 5 HOH A 5 541 541 HOH HOH . E 5 HOH A 6 542 542 HOH HOH . E 5 HOH A 7 543 543 HOH HOH . E 5 HOH A 8 544 544 HOH HOH . E 5 HOH A 9 545 545 HOH HOH . E 5 HOH A 10 546 546 HOH HOH . E 5 HOH A 11 547 547 HOH HOH . E 5 HOH A 12 549 549 HOH HOH . E 5 HOH A 13 550 550 HOH HOH . E 5 HOH A 14 551 551 HOH HOH . E 5 HOH A 15 552 552 HOH HOH . E 5 HOH A 16 553 553 HOH HOH . E 5 HOH A 17 554 554 HOH HOH . E 5 HOH A 18 555 555 HOH HOH . E 5 HOH A 19 556 556 HOH HOH . E 5 HOH A 20 557 557 HOH HOH . E 5 HOH A 21 558 558 HOH HOH . E 5 HOH A 22 559 559 HOH HOH . E 5 HOH A 23 560 560 HOH HOH . E 5 HOH A 24 561 561 HOH HOH . E 5 HOH A 25 562 562 HOH HOH . E 5 HOH A 26 563 563 HOH HOH . E 5 HOH A 27 564 564 HOH HOH . E 5 HOH A 28 565 565 HOH HOH . E 5 HOH A 29 566 566 HOH HOH . E 5 HOH A 30 567 567 HOH HOH . E 5 HOH A 31 568 568 HOH HOH . E 5 HOH A 32 569 569 HOH HOH . E 5 HOH A 33 570 570 HOH HOH . E 5 HOH A 34 571 571 HOH HOH . E 5 HOH A 35 572 572 HOH HOH . E 5 HOH A 36 573 573 HOH HOH . E 5 HOH A 37 574 574 HOH HOH . E 5 HOH A 38 575 575 HOH HOH . E 5 HOH A 39 576 576 HOH HOH . E 5 HOH A 40 577 577 HOH HOH . E 5 HOH A 41 578 578 HOH HOH . E 5 HOH A 42 579 579 HOH HOH . E 5 HOH A 43 580 580 HOH HOH . E 5 HOH A 44 581 581 HOH HOH . E 5 HOH A 45 582 582 HOH HOH . E 5 HOH A 46 583 583 HOH HOH . E 5 HOH A 47 584 584 HOH HOH . E 5 HOH A 48 585 585 HOH HOH . E 5 HOH A 49 586 586 HOH HOH . E 5 HOH A 50 587 587 HOH HOH . E 5 HOH A 51 588 588 HOH HOH . E 5 HOH A 52 589 589 HOH HOH . E 5 HOH A 53 590 590 HOH HOH . E 5 HOH A 54 591 591 HOH HOH . E 5 HOH A 55 592 592 HOH HOH . E 5 HOH A 56 593 593 HOH HOH . E 5 HOH A 57 594 594 HOH HOH . E 5 HOH A 58 595 595 HOH HOH . E 5 HOH A 59 596 596 HOH HOH . E 5 HOH A 60 597 597 HOH HOH . E 5 HOH A 61 598 598 HOH HOH . E 5 HOH A 62 599 599 HOH HOH . E 5 HOH A 63 600 600 HOH HOH . E 5 HOH A 64 601 601 HOH HOH . E 5 HOH A 65 602 602 HOH HOH . E 5 HOH A 66 603 603 HOH HOH . E 5 HOH A 67 604 604 HOH HOH . E 5 HOH A 68 605 605 HOH HOH . E 5 HOH A 69 606 606 HOH HOH . E 5 HOH A 70 607 607 HOH HOH . E 5 HOH A 71 608 608 HOH HOH . E 5 HOH A 72 609 609 HOH HOH . E 5 HOH A 73 610 610 HOH HOH . E 5 HOH A 74 611 611 HOH HOH . E 5 HOH A 75 612 612 HOH HOH . E 5 HOH A 76 614 614 HOH HOH . E 5 HOH A 77 615 615 HOH HOH . E 5 HOH A 78 616 616 HOH HOH . E 5 HOH A 79 617 617 HOH HOH . E 5 HOH A 80 618 618 HOH HOH . E 5 HOH A 81 619 619 HOH HOH . E 5 HOH A 82 620 620 HOH HOH . E 5 HOH A 83 621 621 HOH HOH . E 5 HOH A 84 622 622 HOH HOH . E 5 HOH A 85 623 623 HOH HOH . E 5 HOH A 86 624 624 HOH HOH . E 5 HOH A 87 625 625 HOH HOH . E 5 HOH A 88 626 626 HOH HOH . E 5 HOH A 89 627 627 HOH HOH . E 5 HOH A 90 628 628 HOH HOH . E 5 HOH A 91 629 629 HOH HOH . E 5 HOH A 92 631 631 HOH HOH . E 5 HOH A 93 632 632 HOH HOH . E 5 HOH A 94 633 633 HOH HOH . E 5 HOH A 95 634 634 HOH HOH . E 5 HOH A 96 636 636 HOH HOH . E 5 HOH A 97 637 637 HOH HOH . E 5 HOH A 98 638 638 HOH HOH . E 5 HOH A 99 639 639 HOH HOH . E 5 HOH A 100 640 640 HOH HOH . E 5 HOH A 101 641 641 HOH HOH . E 5 HOH A 102 642 642 HOH HOH . E 5 HOH A 103 643 643 HOH HOH . E 5 HOH A 104 645 645 HOH HOH . E 5 HOH A 105 646 646 HOH HOH . E 5 HOH A 106 647 647 HOH HOH . E 5 HOH A 107 649 649 HOH HOH . E 5 HOH A 108 650 650 HOH HOH . E 5 HOH A 109 651 651 HOH HOH . E 5 HOH A 110 652 652 HOH HOH . E 5 HOH A 111 653 653 HOH HOH . E 5 HOH A 112 654 654 HOH HOH . E 5 HOH A 113 655 655 HOH HOH . E 5 HOH A 114 657 657 HOH HOH . E 5 HOH A 115 658 658 HOH HOH . E 5 HOH A 116 659 659 HOH HOH . E 5 HOH A 117 660 660 HOH HOH . E 5 HOH A 118 661 661 HOH HOH . E 5 HOH A 119 662 662 HOH HOH . E 5 HOH A 120 663 663 HOH HOH . E 5 HOH A 121 664 664 HOH HOH . E 5 HOH A 122 665 665 HOH HOH . E 5 HOH A 123 666 666 HOH HOH . E 5 HOH A 124 667 667 HOH HOH . E 5 HOH A 125 668 668 HOH HOH . E 5 HOH A 126 669 669 HOH HOH . E 5 HOH A 127 670 670 HOH HOH . E 5 HOH A 128 671 671 HOH HOH . E 5 HOH A 129 672 672 HOH HOH . E 5 HOH A 130 673 673 HOH HOH . E 5 HOH A 131 674 674 HOH HOH . E 5 HOH A 132 676 676 HOH HOH . E 5 HOH A 133 677 677 HOH HOH . E 5 HOH A 134 678 678 HOH HOH . E 5 HOH A 135 681 681 HOH HOH . E 5 HOH A 136 682 682 HOH HOH . E 5 HOH A 137 683 683 HOH HOH . E 5 HOH A 138 684 684 HOH HOH . E 5 HOH A 139 685 685 HOH HOH . E 5 HOH A 140 686 686 HOH HOH . E 5 HOH A 141 687 687 HOH HOH . E 5 HOH A 142 689 689 HOH HOH . E 5 HOH A 143 690 690 HOH HOH . E 5 HOH A 144 691 691 HOH HOH . E 5 HOH A 145 692 692 HOH HOH . E 5 HOH A 146 693 693 HOH HOH . E 5 HOH A 147 695 695 HOH HOH . E 5 HOH A 148 696 696 HOH HOH . E 5 HOH A 149 697 697 HOH HOH . E 5 HOH A 150 698 698 HOH HOH . E 5 HOH A 151 699 699 HOH HOH . E 5 HOH A 152 700 700 HOH HOH . E 5 HOH A 153 701 701 HOH HOH . E 5 HOH A 154 702 702 HOH HOH . E 5 HOH A 155 703 703 HOH HOH . E 5 HOH A 156 704 704 HOH HOH . E 5 HOH A 157 706 706 HOH HOH . E 5 HOH A 158 707 707 HOH HOH . E 5 HOH A 159 708 708 HOH HOH . E 5 HOH A 160 710 710 HOH HOH . E 5 HOH A 161 711 711 HOH HOH . E 5 HOH A 162 712 712 HOH HOH . E 5 HOH A 163 713 713 HOH HOH . E 5 HOH A 164 714 714 HOH HOH . E 5 HOH A 165 715 715 HOH HOH . E 5 HOH A 166 716 716 HOH HOH . E 5 HOH A 167 717 717 HOH HOH . E 5 HOH A 168 718 718 HOH HOH . E 5 HOH A 169 719 719 HOH HOH . E 5 HOH A 170 720 720 HOH HOH . E 5 HOH A 171 721 721 HOH HOH . E 5 HOH A 172 722 722 HOH HOH . E 5 HOH A 173 725 725 HOH HOH . E 5 HOH A 174 728 728 HOH HOH . E 5 HOH A 175 729 729 HOH HOH . E 5 HOH A 176 731 731 HOH HOH . E 5 HOH A 177 732 732 HOH HOH . E 5 HOH A 178 733 733 HOH HOH . E 5 HOH A 179 734 734 HOH HOH . E 5 HOH A 180 735 735 HOH HOH . E 5 HOH A 181 736 736 HOH HOH . E 5 HOH A 182 737 737 HOH HOH . E 5 HOH A 183 738 738 HOH HOH . E 5 HOH A 184 739 739 HOH HOH . E 5 HOH A 185 740 740 HOH HOH . E 5 HOH A 186 743 743 HOH HOH . E 5 HOH A 187 745 745 HOH HOH . E 5 HOH A 188 746 746 HOH HOH . E 5 HOH A 189 747 747 HOH HOH . E 5 HOH A 190 748 748 HOH HOH . E 5 HOH A 191 749 749 HOH HOH . E 5 HOH A 192 750 750 HOH HOH . E 5 HOH A 193 752 752 HOH HOH . E 5 HOH A 194 753 753 HOH HOH . E 5 HOH A 195 754 754 HOH HOH . E 5 HOH A 196 755 755 HOH HOH . E 5 HOH A 197 756 756 HOH HOH . E 5 HOH A 198 757 757 HOH HOH . E 5 HOH A 199 758 758 HOH HOH . E 5 HOH A 200 759 759 HOH HOH . E 5 HOH A 201 761 761 HOH HOH . E 5 HOH A 202 762 762 HOH HOH . E 5 HOH A 203 763 763 HOH HOH . E 5 HOH A 204 764 764 HOH HOH . E 5 HOH A 205 766 766 HOH HOH . E 5 HOH A 206 767 767 HOH HOH . E 5 HOH A 207 768 768 HOH HOH . E 5 HOH A 208 771 771 HOH HOH . E 5 HOH A 209 772 772 HOH HOH . E 5 HOH A 210 773 773 HOH HOH . E 5 HOH A 211 774 774 HOH HOH . E 5 HOH A 212 775 775 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 -14.618 -7.386 -48.943 1 55.56 ? N1 PLP 534 A 1 HETATM 2 C C2 PLP . . . B 2 -15.93 -7.102 -48.828 1 55.24 ? C2 PLP 534 A 1 HETATM 3 C C2A PLP . . . B 2 -16.901 -7.587 -49.865 1 55.78 ? C2A PLP 534 A 1 HETATM 4 C C3 PLP . . . B 2 -16.425 -6.302 -47.68 1 55.89 ? C3 PLP 534 A 1 HETATM 5 O O3 PLP . . . B 2 -17.742 -5.99 -47.53 1 56.06 ? O3 PLP 534 A 1 HETATM 6 C C4 PLP . . . B 2 -15.412 -5.861 -46.698 1 57.03 ? C4 PLP 534 A 1 HETATM 7 C C4A PLP . . . B 2 -15.786 -5.073 -45.516 1 56.84 ? C4A PLP 534 A 1 HETATM 8 C C5 PLP . . . B 2 -13.999 -6.242 -46.932 1 55.34 ? C5 PLP 534 A 1 HETATM 9 C C6 PLP . . . B 2 -13.675 -6.994 -48.06 1 54.1 ? C6 PLP 534 A 1 HETATM 10 C C5A PLP . . . B 2 -12.94 -5.815 -45.946 1 52.05 ? C5A PLP 534 A 1 HETATM 11 O O4P PLP . . . B 2 -12.259 -4.655 -46.413 1 41.11 ? O4P PLP 534 A 1 HETATM 12 P P PLP . . . B 2 -10.859 -4.252 -45.734 1 34.44 ? P PLP 534 A 1 HETATM 13 O O1P PLP . . . B 2 -10.183 -5.579 -45.514 1 32.33 ? O1P PLP 534 A 1 HETATM 14 O O2P PLP . . . B 2 -11.324 -3.556 -44.482 1 34.34 ? O2P PLP 534 A 1 HETATM 15 O O3P PLP . . . B 2 -10.178 -3.365 -46.746 1 31.74 ? O3P PLP 534 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #