data_1V72 # _model_server_result.job_id aiLx4QUCLhU6MtrvkzUdEQ _model_server_result.datetime_utc '2024-11-05 00:31:44' _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 1v72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":513}' # _entry.id 1V72 # _exptl.entry_id 1V72 _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 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 1V72 _cell.length_a 95.489 _cell.length_b 95.489 _cell.length_c 107.115 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V72 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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,D _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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 95.489 95.489 0 3 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 107.115 4 'crystal symmetry operation' 8_666 -y+1,-x+1,-z+1 0 -1 0 -1 0 0 0 0 -1 95.489 95.489 107.115 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 212 A LYS 212 1_555 C C4A PLP . A PLP 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? metalc ? metalc1 A OE2 GLU 163 A GLU 163 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc2 A OE1 GLU 163 A GLU 163 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc3 A OD2 ASP 167 A ASP 167 1_555 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc4 A ND1 HIS 341 A HIS 341 5_646 B ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc5 B ZN ZN . A ZN 401 1_555 D O HOH . A HOH 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? # _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 1V72 _atom_sites.fract_transf_matrix[1][1] 0.010472 _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] 0.010472 _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] 0.009336 _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 ZN A 1 401 401 ZN ZN . C 3 PLP A 1 513 513 PLP PLP . D 4 HOH A 1 514 1 HOH HOH . D 4 HOH A 2 515 2 HOH HOH . D 4 HOH A 3 516 3 HOH HOH . D 4 HOH A 4 517 4 HOH HOH . D 4 HOH A 5 518 5 HOH HOH . D 4 HOH A 6 519 6 HOH HOH . D 4 HOH A 7 520 7 HOH HOH . D 4 HOH A 8 521 8 HOH HOH . D 4 HOH A 9 522 9 HOH HOH . D 4 HOH A 10 523 10 HOH HOH . D 4 HOH A 11 524 11 HOH HOH . D 4 HOH A 12 525 12 HOH HOH . D 4 HOH A 13 526 13 HOH HOH . D 4 HOH A 14 527 14 HOH HOH . D 4 HOH A 15 528 15 HOH HOH . D 4 HOH A 16 529 16 HOH HOH . D 4 HOH A 17 530 17 HOH HOH . D 4 HOH A 18 531 18 HOH HOH . D 4 HOH A 19 532 19 HOH HOH . D 4 HOH A 20 533 20 HOH HOH . D 4 HOH A 21 534 21 HOH HOH . D 4 HOH A 22 535 22 HOH HOH . D 4 HOH A 23 536 23 HOH HOH . D 4 HOH A 24 537 24 HOH HOH . D 4 HOH A 25 538 25 HOH HOH . D 4 HOH A 26 539 26 HOH HOH . D 4 HOH A 27 540 27 HOH HOH . D 4 HOH A 28 541 28 HOH HOH . D 4 HOH A 29 542 29 HOH HOH . D 4 HOH A 30 543 30 HOH HOH . D 4 HOH A 31 544 31 HOH HOH . D 4 HOH A 32 545 32 HOH HOH . D 4 HOH A 33 546 33 HOH HOH . D 4 HOH A 34 547 34 HOH HOH . D 4 HOH A 35 548 35 HOH HOH . D 4 HOH A 36 549 36 HOH HOH . D 4 HOH A 37 550 37 HOH HOH . D 4 HOH A 38 551 38 HOH HOH . D 4 HOH A 39 552 39 HOH HOH . D 4 HOH A 40 553 40 HOH HOH . D 4 HOH A 41 554 41 HOH HOH . D 4 HOH A 42 555 42 HOH HOH . D 4 HOH A 43 556 43 HOH HOH . D 4 HOH A 44 557 44 HOH HOH . D 4 HOH A 45 558 46 HOH HOH . D 4 HOH A 46 559 47 HOH HOH . D 4 HOH A 47 560 48 HOH HOH . D 4 HOH A 48 561 49 HOH HOH . D 4 HOH A 49 562 50 HOH HOH . D 4 HOH A 50 563 51 HOH HOH . D 4 HOH A 51 564 52 HOH HOH . D 4 HOH A 52 565 53 HOH HOH . D 4 HOH A 53 566 54 HOH HOH . D 4 HOH A 54 567 55 HOH HOH . D 4 HOH A 55 568 56 HOH HOH . D 4 HOH A 56 569 57 HOH HOH . D 4 HOH A 57 570 58 HOH HOH . D 4 HOH A 58 571 59 HOH HOH . D 4 HOH A 59 572 60 HOH HOH . D 4 HOH A 60 573 61 HOH HOH . D 4 HOH A 61 574 62 HOH HOH . D 4 HOH A 62 575 63 HOH HOH . D 4 HOH A 63 576 64 HOH HOH . D 4 HOH A 64 577 65 HOH HOH . D 4 HOH A 65 578 66 HOH HOH . D 4 HOH A 66 579 67 HOH HOH . D 4 HOH A 67 580 68 HOH HOH . D 4 HOH A 68 581 69 HOH HOH . D 4 HOH A 69 582 70 HOH HOH . D 4 HOH A 70 583 71 HOH HOH . D 4 HOH A 71 584 72 HOH HOH . D 4 HOH A 72 585 73 HOH HOH . D 4 HOH A 73 586 74 HOH HOH . D 4 HOH A 74 587 75 HOH HOH . D 4 HOH A 75 588 76 HOH HOH . D 4 HOH A 76 589 77 HOH HOH . D 4 HOH A 77 590 78 HOH HOH . D 4 HOH A 78 591 79 HOH HOH . D 4 HOH A 79 592 80 HOH HOH . D 4 HOH A 80 593 81 HOH HOH . D 4 HOH A 81 594 82 HOH HOH . D 4 HOH A 82 595 83 HOH HOH . D 4 HOH A 83 596 84 HOH HOH . D 4 HOH A 84 597 85 HOH HOH . D 4 HOH A 85 598 86 HOH HOH . D 4 HOH A 86 599 87 HOH HOH . D 4 HOH A 87 600 88 HOH HOH . D 4 HOH A 88 601 89 HOH HOH . D 4 HOH A 89 602 90 HOH HOH . D 4 HOH A 90 603 91 HOH HOH . D 4 HOH A 91 604 92 HOH HOH . D 4 HOH A 92 605 93 HOH HOH . D 4 HOH A 93 606 94 HOH HOH . D 4 HOH A 94 607 95 HOH HOH . D 4 HOH A 95 608 96 HOH HOH . D 4 HOH A 96 609 97 HOH HOH . D 4 HOH A 97 610 98 HOH HOH . D 4 HOH A 98 611 99 HOH HOH . D 4 HOH A 99 612 100 HOH HOH . D 4 HOH A 100 613 101 HOH HOH . D 4 HOH A 101 614 102 HOH HOH . D 4 HOH A 102 615 103 HOH HOH . D 4 HOH A 103 616 104 HOH HOH . D 4 HOH A 104 617 105 HOH HOH . D 4 HOH A 105 618 106 HOH HOH . D 4 HOH A 106 619 107 HOH HOH . D 4 HOH A 107 620 108 HOH HOH . D 4 HOH A 108 621 109 HOH HOH . D 4 HOH A 109 622 110 HOH HOH . D 4 HOH A 110 623 111 HOH HOH . D 4 HOH A 111 624 112 HOH HOH . D 4 HOH A 112 625 113 HOH HOH . D 4 HOH A 113 626 114 HOH HOH . D 4 HOH A 114 627 115 HOH HOH . D 4 HOH A 115 628 116 HOH HOH . D 4 HOH A 116 629 117 HOH HOH . D 4 HOH A 117 630 118 HOH HOH . D 4 HOH A 118 631 119 HOH HOH . D 4 HOH A 119 632 120 HOH HOH . D 4 HOH A 120 633 121 HOH HOH . D 4 HOH A 121 634 122 HOH HOH . D 4 HOH A 122 635 123 HOH HOH . D 4 HOH A 123 636 124 HOH HOH . D 4 HOH A 124 637 125 HOH HOH . D 4 HOH A 125 638 126 HOH HOH . D 4 HOH A 126 639 127 HOH HOH . D 4 HOH A 127 640 128 HOH HOH . D 4 HOH A 128 641 129 HOH HOH . D 4 HOH A 129 642 130 HOH HOH . D 4 HOH A 130 643 131 HOH HOH . D 4 HOH A 131 644 132 HOH HOH . D 4 HOH A 132 645 133 HOH HOH . D 4 HOH A 133 646 134 HOH HOH . D 4 HOH A 134 647 135 HOH HOH . D 4 HOH A 135 648 136 HOH HOH . D 4 HOH A 136 649 137 HOH HOH . D 4 HOH A 137 650 138 HOH HOH . D 4 HOH A 138 651 139 HOH HOH . D 4 HOH A 139 652 140 HOH HOH . D 4 HOH A 140 653 141 HOH HOH . D 4 HOH A 141 654 142 HOH HOH . D 4 HOH A 142 655 143 HOH HOH . D 4 HOH A 143 656 144 HOH HOH . D 4 HOH A 144 657 145 HOH HOH . D 4 HOH A 145 658 146 HOH HOH . D 4 HOH A 146 659 147 HOH HOH . D 4 HOH A 147 660 148 HOH HOH . D 4 HOH A 148 661 149 HOH HOH . D 4 HOH A 149 662 150 HOH HOH . D 4 HOH A 150 663 151 HOH HOH . D 4 HOH A 151 664 152 HOH HOH . D 4 HOH A 152 665 153 HOH HOH . D 4 HOH A 153 666 154 HOH HOH . D 4 HOH A 154 667 155 HOH HOH . D 4 HOH A 155 668 156 HOH HOH . D 4 HOH A 156 669 157 HOH HOH . D 4 HOH A 157 670 158 HOH HOH . D 4 HOH A 158 671 159 HOH HOH . D 4 HOH A 159 672 160 HOH HOH . D 4 HOH A 160 673 161 HOH HOH . D 4 HOH A 161 674 162 HOH HOH . D 4 HOH A 162 675 163 HOH HOH . D 4 HOH A 163 676 164 HOH HOH . D 4 HOH A 164 677 165 HOH HOH . D 4 HOH A 165 678 167 HOH HOH . D 4 HOH A 166 679 168 HOH HOH . D 4 HOH A 167 680 170 HOH HOH . D 4 HOH A 168 681 171 HOH HOH . D 4 HOH A 169 682 172 HOH HOH . D 4 HOH A 170 683 173 HOH HOH . D 4 HOH A 171 684 174 HOH HOH . D 4 HOH A 172 685 175 HOH HOH . D 4 HOH A 173 686 176 HOH HOH . D 4 HOH A 174 687 177 HOH HOH . D 4 HOH A 175 688 178 HOH HOH . D 4 HOH A 176 689 180 HOH HOH . D 4 HOH A 177 690 181 HOH HOH . D 4 HOH A 178 691 182 HOH HOH . D 4 HOH A 179 692 183 HOH HOH . D 4 HOH A 180 693 184 HOH HOH . D 4 HOH A 181 694 185 HOH HOH . D 4 HOH A 182 695 186 HOH HOH . D 4 HOH A 183 696 188 HOH HOH . D 4 HOH A 184 697 189 HOH HOH . D 4 HOH A 185 698 190 HOH HOH . D 4 HOH A 186 699 191 HOH HOH . D 4 HOH A 187 700 192 HOH HOH . D 4 HOH A 188 701 193 HOH HOH . D 4 HOH A 189 702 194 HOH HOH . D 4 HOH A 190 703 195 HOH HOH . D 4 HOH A 191 704 196 HOH HOH . D 4 HOH A 192 705 197 HOH HOH . D 4 HOH A 193 706 198 HOH HOH . D 4 HOH A 194 707 199 HOH HOH . D 4 HOH A 195 708 200 HOH HOH . D 4 HOH A 196 709 201 HOH HOH . D 4 HOH A 197 710 202 HOH HOH . D 4 HOH A 198 711 203 HOH HOH . D 4 HOH A 199 712 205 HOH HOH . D 4 HOH A 200 713 206 HOH HOH . D 4 HOH A 201 714 208 HOH HOH . D 4 HOH A 202 715 209 HOH HOH . D 4 HOH A 203 716 210 HOH HOH . D 4 HOH A 204 717 211 HOH HOH . D 4 HOH A 205 718 212 HOH HOH . D 4 HOH A 206 719 213 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 . . . C 3 62.323 57.888 68.24 1 24.43 ? N1 PLP 513 A 1 HETATM 2 C C2 PLP . . . C 3 62.582 58.601 69.373 1 25.78 ? C2 PLP 513 A 1 HETATM 3 C C2A PLP . . . C 3 62.718 57.834 70.706 1 27.05 ? C2A PLP 513 A 1 HETATM 4 C C3 PLP . . . C 3 62.731 59.983 69.307 1 26.06 ? C3 PLP 513 A 1 HETATM 5 O O3 PLP . . . C 3 63.001 60.702 70.458 1 27.38 ? O3 PLP 513 A 1 HETATM 6 C C4 PLP . . . C 3 62.616 60.641 68.065 1 26.05 ? C4 PLP 513 A 1 HETATM 7 C C4A PLP . . . C 3 62.823 62.159 68.014 1 26.62 ? C4A PLP 513 A 1 HETATM 8 C C5 PLP . . . C 3 62.347 59.87 66.903 1 24.94 ? C5 PLP 513 A 1 HETATM 9 C C6 PLP . . . C 3 62.203 58.518 67.012 1 24.45 ? C6 PLP 513 A 1 HETATM 10 C C5A PLP . . . C 3 62.221 60.444 65.481 1 24.85 ? C5A PLP 513 A 1 HETATM 11 O O4P PLP . . . C 3 61.275 61.406 65.163 1 23.45 ? O4P PLP 513 A 1 HETATM 12 P P PLP . . . C 3 61.285 62.142 63.745 1 21.68 ? P PLP 513 A 1 HETATM 13 O O1P PLP . . . C 3 60.536 63.37 63.996 1 23.6 ? O1P PLP 513 A 1 HETATM 14 O O2P PLP . . . C 3 60.403 61.124 62.899 1 21.69 ? O2P PLP 513 A 1 HETATM 15 O O3P PLP . . . C 3 62.629 62.189 63.108 1 22.87 ? O3P PLP 513 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #