data_6MRI # _model_server_result.job_id uTMAqR4r8NsR8eQt5dh6hA _model_server_result.datetime_utc '2024-11-27 23:27:58' _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 6mri # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 6MRI # _exptl.entry_id 6MRI _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 6MRI _cell.length_a 125.73 _cell.length_b 125.73 _cell.length_c 138.55 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MRI _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 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 # 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 240 A LYS 226 1_555 B C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 A C HIS 377 A HIS 363 1_555 A N CSS 378 A CSS 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C CSS 378 A CSS 364 1_555 A N ALA 379 A ALA 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _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 274 n y N1 C6 PLP sing 275 n y C2 C2A PLP sing 276 n n C2 C3 PLP sing 277 n y C2A H2A1 PLP sing 278 n n C2A H2A2 PLP sing 279 n n C2A H2A3 PLP sing 280 n n C3 O3 PLP sing 281 n n C3 C4 PLP doub 282 n y O3 HO3 PLP sing 283 n n C4 C4A PLP sing 284 n n C4 C5 PLP sing 285 n y C4A O4A PLP doub 286 n n C4A H4A PLP sing 287 n n C5 C6 PLP doub 288 n y C5 C5A PLP sing 289 n n C6 H6 PLP sing 290 n n C5A O4P PLP sing 291 n n C5A H5A1 PLP sing 292 n n C5A H5A2 PLP sing 293 n n O4P P PLP sing 294 n n P O1P PLP doub 295 n n P O2P PLP sing 296 n n P O3P PLP sing 297 n n O2P HOP2 PLP sing 298 n n O3P HOP3 PLP sing 299 n n # _atom_sites.entry_id 6MRI _atom_sites.fract_transf_matrix[1][1] 0.007954 _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] 0.007954 _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] 0.007218 _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 1 500 500 PLP PLP . C 3 HOH A 1 601 553 HOH HOH . C 3 HOH A 2 602 580 HOH HOH . C 3 HOH A 3 603 535 HOH HOH . C 3 HOH A 4 604 505 HOH HOH . C 3 HOH A 5 605 562 HOH HOH . C 3 HOH A 6 606 534 HOH HOH . C 3 HOH A 7 607 506 HOH HOH . C 3 HOH A 8 608 557 HOH HOH . C 3 HOH A 9 609 585 HOH HOH . C 3 HOH A 10 610 511 HOH HOH . C 3 HOH A 11 611 510 HOH HOH . C 3 HOH A 12 612 520 HOH HOH . C 3 HOH A 13 613 1003 HOH HOH . C 3 HOH A 14 614 523 HOH HOH . C 3 HOH A 15 615 507 HOH HOH . C 3 HOH A 16 616 541 HOH HOH . C 3 HOH A 17 617 552 HOH HOH . C 3 HOH A 18 618 515 HOH HOH . C 3 HOH A 19 619 530 HOH HOH . C 3 HOH A 20 620 570 HOH HOH . C 3 HOH A 21 621 528 HOH HOH . C 3 HOH A 22 622 518 HOH HOH . C 3 HOH A 23 623 568 HOH HOH . C 3 HOH A 24 624 508 HOH HOH . C 3 HOH A 25 625 513 HOH HOH . C 3 HOH A 26 626 554 HOH HOH . C 3 HOH A 27 627 533 HOH HOH . C 3 HOH A 28 628 551 HOH HOH . C 3 HOH A 29 629 525 HOH HOH . C 3 HOH A 30 630 542 HOH HOH . C 3 HOH A 31 631 532 HOH HOH . C 3 HOH A 32 632 543 HOH HOH . C 3 HOH A 33 633 512 HOH HOH . C 3 HOH A 34 634 536 HOH HOH . C 3 HOH A 35 635 503 HOH HOH . C 3 HOH A 36 636 555 HOH HOH . C 3 HOH A 37 637 566 HOH HOH . C 3 HOH A 38 638 545 HOH HOH . C 3 HOH A 39 639 546 HOH HOH . C 3 HOH A 40 640 577 HOH HOH . C 3 HOH A 41 641 538 HOH HOH . C 3 HOH A 42 642 540 HOH HOH . C 3 HOH A 43 643 579 HOH HOH . C 3 HOH A 44 644 567 HOH HOH . C 3 HOH A 45 645 537 HOH HOH . C 3 HOH A 46 646 559 HOH HOH . C 3 HOH A 47 647 527 HOH HOH . C 3 HOH A 48 648 558 HOH HOH . C 3 HOH A 49 649 517 HOH HOH . C 3 HOH A 50 650 583 HOH HOH . C 3 HOH A 51 651 531 HOH HOH . C 3 HOH A 52 652 547 HOH HOH . C 3 HOH A 53 653 549 HOH HOH . C 3 HOH A 54 654 560 HOH HOH . C 3 HOH A 55 655 548 HOH HOH . C 3 HOH A 56 656 514 HOH HOH . C 3 HOH A 57 657 569 HOH HOH . C 3 HOH A 58 658 578 HOH HOH . C 3 HOH A 59 659 581 HOH HOH . C 3 HOH A 60 660 516 HOH HOH . C 3 HOH A 61 661 563 HOH HOH . C 3 HOH A 62 662 521 HOH HOH . C 3 HOH A 63 663 556 HOH HOH . C 3 HOH A 64 664 576 HOH HOH . C 3 HOH A 65 665 572 HOH HOH . C 3 HOH A 66 666 522 HOH HOH . C 3 HOH A 67 667 509 HOH HOH . C 3 HOH A 68 668 550 HOH HOH . C 3 HOH A 69 669 539 HOH HOH . C 3 HOH A 70 670 526 HOH HOH . C 3 HOH A 71 671 573 HOH HOH . C 3 HOH A 72 672 575 HOH HOH . C 3 HOH A 73 673 564 HOH HOH . C 3 HOH A 74 674 524 HOH HOH . C 3 HOH A 75 675 504 HOH HOH . C 3 HOH A 76 676 574 HOH HOH . C 3 HOH A 77 677 565 HOH HOH . C 3 HOH A 78 678 561 HOH HOH . C 3 HOH A 79 679 544 HOH HOH . C 3 HOH A 80 680 582 HOH HOH . C 3 HOH A 81 681 529 HOH HOH . C 3 HOH A 82 682 571 HOH HOH . C 3 HOH A 83 683 519 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 25.547 45.297 7.761 1 43.05 ? N1 PLP 500 A 1 HETATM 2 C C2 PLP . . . B 2 25.704 46.619 8.079 1 48.5 ? C2 PLP 500 A 1 HETATM 3 C C2A PLP . . . B 2 24.952 47.148 9.254 1 44.75 ? C2A PLP 500 A 1 HETATM 4 C C3 PLP . . . B 2 26.567 47.437 7.338 1 55.09 ? C3 PLP 500 A 1 HETATM 5 O O3 PLP . . . B 2 26.739 48.773 7.667 1 52.16 ? O3 PLP 500 A 1 HETATM 6 C C4 PLP . . . B 2 27.268 46.885 6.26 1 52.65 ? C4 PLP 500 A 1 HETATM 7 C C4A PLP . . . B 2 27.906 47.775 5.222 1 54.15 ? C4A PLP 500 A 1 HETATM 8 C C5 PLP . . . B 2 27.083 45.548 5.95 1 46.44 ? C5 PLP 500 A 1 HETATM 9 C C6 PLP . . . B 2 26.231 44.762 6.697 1 44.92 ? C6 PLP 500 A 1 HETATM 10 C C5A PLP . . . B 2 27.816 44.936 4.786 1 51.06 ? C5A PLP 500 A 1 HETATM 11 O O4P PLP . . . B 2 29.165 44.694 5.122 1 53.47 ? O4P PLP 500 A 1 HETATM 12 P P PLP . . . B 2 30.244 44.437 3.962 1 51.41 ? P PLP 500 A 1 HETATM 13 O O1P PLP . . . B 2 29.963 45.341 2.789 1 55.96 ? O1P PLP 500 A 1 HETATM 14 O O2P PLP . . . B 2 30.194 43.005 3.468 1 49.59 ? O2P PLP 500 A 1 HETATM 15 O O3P PLP . . . B 2 31.569 44.779 4.582 1 50.35 ? O3P PLP 500 A 1 HETATM 16 H H2A1 PLP . . . B 2 25.205 48.197 9.405 1 53.78 ? H2A1 PLP 500 A 1 HETATM 17 H H2A2 PLP . . . B 2 25.22 46.578 10.144 1 53.78 ? H2A2 PLP 500 A 1 HETATM 18 H H2A3 PLP . . . B 2 23.881 47.055 9.072 1 53.78 ? H2A3 PLP 500 A 1 HETATM 19 H HO3 PLP . . . B 2 27.468 49.149 7.132 1 62.67 ? HO3 PLP 500 A 1 HETATM 20 H H6 PLP . . . B 2 26.1 43.711 6.441 1 53.98 ? H6 PLP 500 A 1 HETATM 21 H H5A1 PLP . . . B 2 27.335 43.999 4.503 1 61.35 ? H5A1 PLP 500 A 1 HETATM 22 H H5A2 PLP . . . B 2 27.767 45.609 3.929 1 61.35 ? H5A2 PLP 500 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #