data_1V2D # _model_server_result.job_id c7bsyEZqpQjpAMzQcQOjRQ _model_server_result.datetime_utc '2024-11-23 23:17:28' _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 1v2d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":510}' # _entry.id 1V2D # _exptl.entry_id 1V2D _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 1V2D _cell.length_a 77.8 _cell.length_b 91.9 _cell.length_c 110.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V2D _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 77.8 0 55.35 # _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 222 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 222 _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 510 _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 1.371 _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 1V2D _atom_sites.fract_transf_matrix[1][1] 0.012853 _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] 0.010881 _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] 0.009033 _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 1 510 510 PLP PLP . C 3 HOH A 1 511 1 HOH HOH . C 3 HOH A 2 512 2 HOH HOH . C 3 HOH A 3 513 3 HOH HOH . C 3 HOH A 4 514 4 HOH HOH . C 3 HOH A 5 515 5 HOH HOH . C 3 HOH A 6 516 6 HOH HOH . C 3 HOH A 7 517 7 HOH HOH . C 3 HOH A 8 518 8 HOH HOH . C 3 HOH A 9 519 9 HOH HOH . C 3 HOH A 10 520 10 HOH HOH . C 3 HOH A 11 521 11 HOH HOH . C 3 HOH A 12 522 12 HOH HOH . C 3 HOH A 13 523 13 HOH HOH . C 3 HOH A 14 524 14 HOH HOH . C 3 HOH A 15 525 15 HOH HOH . C 3 HOH A 16 526 16 HOH HOH . C 3 HOH A 17 527 17 HOH HOH . C 3 HOH A 18 528 18 HOH HOH . C 3 HOH A 19 529 19 HOH HOH . C 3 HOH A 20 530 20 HOH HOH . C 3 HOH A 21 531 21 HOH HOH . C 3 HOH A 22 532 22 HOH HOH . C 3 HOH A 23 533 23 HOH HOH . C 3 HOH A 24 534 24 HOH HOH . C 3 HOH A 25 535 25 HOH HOH . C 3 HOH A 26 536 26 HOH HOH . C 3 HOH A 27 537 27 HOH HOH . C 3 HOH A 28 538 28 HOH HOH . C 3 HOH A 29 539 29 HOH HOH . C 3 HOH A 30 540 30 HOH HOH . C 3 HOH A 31 541 31 HOH HOH . C 3 HOH A 32 542 32 HOH HOH . C 3 HOH A 33 543 33 HOH HOH . C 3 HOH A 34 544 34 HOH HOH . C 3 HOH A 35 545 35 HOH HOH . C 3 HOH A 36 546 36 HOH HOH . C 3 HOH A 37 547 37 HOH HOH . C 3 HOH A 38 548 38 HOH HOH . C 3 HOH A 39 549 39 HOH HOH . C 3 HOH A 40 550 40 HOH HOH . C 3 HOH A 41 551 41 HOH HOH . C 3 HOH A 42 552 42 HOH HOH . C 3 HOH A 43 553 43 HOH HOH . C 3 HOH A 44 554 44 HOH HOH . C 3 HOH A 45 555 45 HOH HOH . C 3 HOH A 46 556 46 HOH HOH . C 3 HOH A 47 557 47 HOH HOH . C 3 HOH A 48 558 48 HOH HOH . C 3 HOH A 49 559 49 HOH HOH . C 3 HOH A 50 560 50 HOH HOH . C 3 HOH A 51 561 51 HOH HOH . C 3 HOH A 52 562 52 HOH HOH . C 3 HOH A 53 563 53 HOH HOH . C 3 HOH A 54 564 54 HOH HOH . C 3 HOH A 55 565 55 HOH HOH . C 3 HOH A 56 566 56 HOH HOH . C 3 HOH A 57 567 57 HOH HOH . C 3 HOH A 58 568 58 HOH HOH . C 3 HOH A 59 569 59 HOH HOH . C 3 HOH A 60 570 60 HOH HOH . C 3 HOH A 61 571 61 HOH HOH . C 3 HOH A 62 572 62 HOH HOH . C 3 HOH A 63 573 63 HOH HOH . C 3 HOH A 64 574 64 HOH HOH . C 3 HOH A 65 575 65 HOH HOH . C 3 HOH A 66 576 66 HOH HOH . C 3 HOH A 67 577 67 HOH HOH . C 3 HOH A 68 578 68 HOH HOH . C 3 HOH A 69 579 69 HOH HOH . C 3 HOH A 70 580 70 HOH HOH . C 3 HOH A 71 581 71 HOH HOH . C 3 HOH A 72 582 72 HOH HOH . C 3 HOH A 73 583 73 HOH HOH . C 3 HOH A 74 584 74 HOH HOH . C 3 HOH A 75 585 75 HOH HOH . C 3 HOH A 76 586 76 HOH HOH . C 3 HOH A 77 587 77 HOH HOH . C 3 HOH A 78 588 78 HOH HOH . C 3 HOH A 79 589 79 HOH HOH . C 3 HOH A 80 590 80 HOH HOH . C 3 HOH A 81 591 81 HOH HOH . C 3 HOH A 82 592 82 HOH HOH . C 3 HOH A 83 593 83 HOH HOH . C 3 HOH A 84 594 84 HOH HOH . C 3 HOH A 85 595 85 HOH HOH . C 3 HOH A 86 596 86 HOH HOH . C 3 HOH A 87 597 87 HOH HOH . C 3 HOH A 88 598 88 HOH HOH . C 3 HOH A 89 599 89 HOH HOH . C 3 HOH A 90 600 90 HOH HOH . C 3 HOH A 91 601 91 HOH HOH . C 3 HOH A 92 602 92 HOH HOH . C 3 HOH A 93 603 93 HOH HOH . C 3 HOH A 94 604 94 HOH HOH . C 3 HOH A 95 605 95 HOH HOH . C 3 HOH A 96 606 96 HOH HOH . C 3 HOH A 97 607 97 HOH HOH . C 3 HOH A 98 608 98 HOH HOH . C 3 HOH A 99 609 99 HOH HOH . C 3 HOH A 100 610 100 HOH HOH . C 3 HOH A 101 611 101 HOH HOH . C 3 HOH A 102 612 102 HOH HOH . C 3 HOH A 103 613 103 HOH HOH . C 3 HOH A 104 614 104 HOH HOH . C 3 HOH A 105 615 105 HOH HOH . C 3 HOH A 106 616 106 HOH HOH . C 3 HOH A 107 617 107 HOH HOH . C 3 HOH A 108 618 108 HOH HOH . C 3 HOH A 109 619 109 HOH HOH . C 3 HOH A 110 620 110 HOH HOH . C 3 HOH A 111 621 111 HOH HOH . C 3 HOH A 112 622 112 HOH HOH . C 3 HOH A 113 623 113 HOH HOH . C 3 HOH A 114 624 114 HOH HOH . C 3 HOH A 115 625 115 HOH HOH . C 3 HOH A 116 626 116 HOH HOH . C 3 HOH A 117 627 117 HOH HOH . C 3 HOH A 118 628 118 HOH HOH . C 3 HOH A 119 629 119 HOH HOH . C 3 HOH A 120 630 120 HOH HOH . C 3 HOH A 121 631 121 HOH HOH . C 3 HOH A 122 632 122 HOH HOH . C 3 HOH A 123 633 123 HOH HOH . C 3 HOH A 124 634 124 HOH HOH . C 3 HOH A 125 635 125 HOH HOH . C 3 HOH A 126 636 126 HOH HOH . C 3 HOH A 127 637 127 HOH HOH . C 3 HOH A 128 638 128 HOH HOH . C 3 HOH A 129 639 129 HOH HOH . C 3 HOH A 130 640 130 HOH HOH . C 3 HOH A 131 641 131 HOH HOH . C 3 HOH A 132 642 132 HOH HOH . C 3 HOH A 133 643 133 HOH HOH . C 3 HOH A 134 644 134 HOH HOH . C 3 HOH A 135 645 135 HOH HOH . C 3 HOH A 136 646 136 HOH HOH . C 3 HOH A 137 647 137 HOH HOH . C 3 HOH A 138 648 138 HOH HOH . C 3 HOH A 139 649 139 HOH HOH . C 3 HOH A 140 650 140 HOH HOH . C 3 HOH A 141 651 141 HOH HOH . C 3 HOH A 142 652 142 HOH HOH . C 3 HOH A 143 653 143 HOH HOH . C 3 HOH A 144 654 144 HOH HOH . C 3 HOH A 145 655 145 HOH HOH . C 3 HOH A 146 656 146 HOH HOH . C 3 HOH A 147 657 147 HOH HOH . C 3 HOH A 148 658 148 HOH HOH . C 3 HOH A 149 659 149 HOH HOH . C 3 HOH A 150 660 150 HOH HOH . C 3 HOH A 151 661 151 HOH HOH . C 3 HOH A 152 662 152 HOH HOH . C 3 HOH A 153 663 153 HOH HOH . C 3 HOH A 154 664 154 HOH HOH . C 3 HOH A 155 665 155 HOH HOH . C 3 HOH A 156 666 156 HOH HOH . C 3 HOH A 157 667 157 HOH HOH . C 3 HOH A 158 668 158 HOH HOH . C 3 HOH A 159 669 159 HOH HOH . C 3 HOH A 160 670 160 HOH HOH . C 3 HOH A 161 671 161 HOH HOH . C 3 HOH A 162 672 162 HOH HOH . C 3 HOH A 163 673 163 HOH HOH . C 3 HOH A 164 674 164 HOH HOH . C 3 HOH A 165 675 165 HOH HOH . C 3 HOH A 166 676 166 HOH HOH . C 3 HOH A 167 677 167 HOH HOH . C 3 HOH A 168 678 168 HOH HOH . C 3 HOH A 169 679 169 HOH HOH . C 3 HOH A 170 680 170 HOH HOH . C 3 HOH A 171 681 171 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 29.92 17.454 15.948 1 11.9 ? N1 PLP 510 A 1 HETATM 2 C C2 PLP . . . B 2 28.814 16.807 15.502 1 10.48 ? C2 PLP 510 A 1 HETATM 3 C C2A PLP . . . B 2 28.049 17.375 14.25 1 6.68 ? C2A PLP 510 A 1 HETATM 4 C C3 PLP . . . B 2 28.39 15.658 16.148 1 11.6 ? C3 PLP 510 A 1 HETATM 5 O O3 PLP . . . B 2 27.271 15.003 15.728 1 10.83 ? O3 PLP 510 A 1 HETATM 6 C C4 PLP . . . B 2 29.083 15.174 17.236 1 11.55 ? C4 PLP 510 A 1 HETATM 7 C C4A PLP . . . B 2 28.604 13.865 17.9 1 13.74 ? C4A PLP 510 A 1 HETATM 8 C C5 PLP . . . B 2 30.229 15.865 17.674 1 12.85 ? C5 PLP 510 A 1 HETATM 9 C C6 PLP . . . B 2 30.629 16.996 17.025 1 11.1 ? C6 PLP 510 A 1 HETATM 10 C C5A PLP . . . B 2 31.05 15.422 18.899 1 11.24 ? C5A PLP 510 A 1 HETATM 11 O O4P PLP . . . B 2 31.834 14.269 18.662 1 10.91 ? O4P PLP 510 A 1 HETATM 12 P P PLP . . . B 2 32.527 13.539 19.916 1 11.82 ? P PLP 510 A 1 HETATM 13 O O1P PLP . . . B 2 33.591 12.704 19.312 1 9.27 ? O1P PLP 510 A 1 HETATM 14 O O2P PLP . . . B 2 31.456 12.599 20.618 1 9.63 ? O2P PLP 510 A 1 HETATM 15 O O3P PLP . . . B 2 32.931 14.583 20.916 1 9.27 ? O3P PLP 510 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #