data_6O12 # _model_server_result.job_id Q9bu7ZsKwbJcWpEYkFrPMw _model_server_result.datetime_utc '2024-11-28 05:22:12' _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 6o12 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6O12 # _exptl.entry_id 6O12 _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 6O12 _cell.length_a 127.28 _cell.length_b 127.28 _cell.length_c 134.163 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6O12 _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,D _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 # _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 226 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 226 _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 501 _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 1.427 _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 6O12 _atom_sites.fract_transf_matrix[1][1] 0.007857 _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] 0.007857 _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] 0.007454 _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 1 501 500 PLP PLP . C 3 CL A 1 502 701 CL CL . D 4 HOH A 1 601 505 HOH HOH . D 4 HOH A 2 602 574 HOH HOH . D 4 HOH A 3 603 554 HOH HOH . D 4 HOH A 4 604 561 HOH HOH . D 4 HOH A 5 605 531 HOH HOH . D 4 HOH A 6 606 544 HOH HOH . D 4 HOH A 7 607 547 HOH HOH . D 4 HOH A 8 608 541 HOH HOH . D 4 HOH A 9 609 582 HOH HOH . D 4 HOH A 10 610 551 HOH HOH . D 4 HOH A 11 611 580 HOH HOH . D 4 HOH A 12 612 565 HOH HOH . D 4 HOH A 13 613 572 HOH HOH . D 4 HOH A 14 614 563 HOH HOH . D 4 HOH A 15 615 527 HOH HOH . D 4 HOH A 16 616 530 HOH HOH . D 4 HOH A 17 617 557 HOH HOH . D 4 HOH A 18 618 509 HOH HOH . D 4 HOH A 19 619 552 HOH HOH . D 4 HOH A 20 620 518 HOH HOH . D 4 HOH A 21 621 508 HOH HOH . D 4 HOH A 22 622 549 HOH HOH . D 4 HOH A 23 623 511 HOH HOH . D 4 HOH A 24 624 519 HOH HOH . D 4 HOH A 25 625 536 HOH HOH . D 4 HOH A 26 626 523 HOH HOH . D 4 HOH A 27 627 562 HOH HOH . D 4 HOH A 28 628 533 HOH HOH . D 4 HOH A 29 629 548 HOH HOH . D 4 HOH A 30 630 573 HOH HOH . D 4 HOH A 31 631 566 HOH HOH . D 4 HOH A 32 632 539 HOH HOH . D 4 HOH A 33 633 515 HOH HOH . D 4 HOH A 34 634 524 HOH HOH . D 4 HOH A 35 635 510 HOH HOH . D 4 HOH A 36 636 558 HOH HOH . D 4 HOH A 37 637 522 HOH HOH . D 4 HOH A 38 638 532 HOH HOH . D 4 HOH A 39 639 564 HOH HOH . D 4 HOH A 40 640 555 HOH HOH . D 4 HOH A 41 641 550 HOH HOH . D 4 HOH A 42 642 520 HOH HOH . D 4 HOH A 43 643 571 HOH HOH . D 4 HOH A 44 644 578 HOH HOH . D 4 HOH A 45 645 543 HOH HOH . D 4 HOH A 46 646 534 HOH HOH . D 4 HOH A 47 647 556 HOH HOH . D 4 HOH A 48 648 537 HOH HOH . D 4 HOH A 49 649 567 HOH HOH . D 4 HOH A 50 650 575 HOH HOH . D 4 HOH A 51 651 559 HOH HOH . D 4 HOH A 52 652 576 HOH HOH . D 4 HOH A 53 653 560 HOH HOH . D 4 HOH A 54 654 569 HOH HOH . D 4 HOH A 55 655 512 HOH HOH . D 4 HOH A 56 656 525 HOH HOH . D 4 HOH A 57 657 528 HOH HOH . D 4 HOH A 58 658 540 HOH HOH . D 4 HOH A 59 659 581 HOH HOH . D 4 HOH A 60 660 517 HOH HOH . D 4 HOH A 61 661 506 HOH HOH . D 4 HOH A 62 662 535 HOH HOH . D 4 HOH A 63 663 583 HOH HOH . D 4 HOH A 64 664 513 HOH HOH . D 4 HOH A 65 665 514 HOH HOH . D 4 HOH A 66 666 516 HOH HOH . D 4 HOH A 67 667 542 HOH HOH . D 4 HOH A 68 668 579 HOH HOH . D 4 HOH A 69 669 553 HOH HOH . D 4 HOH A 70 670 538 HOH HOH . D 4 HOH A 71 671 570 HOH HOH . D 4 HOH A 72 672 526 HOH HOH . D 4 HOH A 73 673 545 HOH HOH . D 4 HOH A 74 674 507 HOH HOH . D 4 HOH A 75 675 504 HOH HOH . D 4 HOH A 76 676 529 HOH HOH . D 4 HOH A 77 677 521 HOH HOH . D 4 HOH A 78 678 503 HOH HOH . D 4 HOH A 79 679 587 HOH HOH . D 4 HOH A 80 680 502 HOH HOH . D 4 HOH A 81 681 584 HOH HOH . D 4 HOH A 82 682 577 HOH HOH . D 4 HOH A 83 683 586 HOH HOH . D 4 HOH A 84 684 546 HOH HOH . D 4 HOH A 85 685 585 HOH HOH . D 4 HOH A 86 686 568 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 26.164 45.883 7.593 1 39.47 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . B 2 26.242 47.216 7.917 1 43.06 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . B 2 25.46 47.737 9.094 1 39.95 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . B 2 27.056 48.061 7.16 1 44.4 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . B 2 27.134 49.386 7.496 1 45.36 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . B 2 27.788 47.555 6.083 1 42.35 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . B 2 28.442 48.459 5.073 1 49.03 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . B 2 27.676 46.21 5.768 1 42.21 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . B 2 26.878 45.371 6.531 1 40.05 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . B 2 28.453 45.661 4.604 1 41.56 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . B 2 29.816 45.478 4.942 1 43.41 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . B 2 30.825 45.007 3.779 1 43.16 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . B 2 30.421 45.767 2.533 1 43.58 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . B 2 30.754 43.51 3.509 1 36.56 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . B 2 32.221 45.355 4.215 1 43.79 ? O3P PLP 501 A 1 HETATM 16 H H2A1 PLP . . . B 2 25.613 48.812 9.185 1 47.94 ? H2A1 PLP 501 A 1 HETATM 17 H H2A2 PLP . . . B 2 25.801 47.243 10.004 1 47.94 ? H2A2 PLP 501 A 1 HETATM 18 H H2A3 PLP . . . B 2 24.4 47.532 8.945 1 47.94 ? H2A3 PLP 501 A 1 HETATM 19 H HO3 PLP . . . B 2 27.588 49.878 6.78 1 54.43 ? HO3 PLP 501 A 1 HETATM 20 H H6 PLP . . . B 2 26.814 44.31 6.291 1 48.07 ? H6 PLP 501 A 1 HETATM 21 H H5A1 PLP . . . B 2 28.023 44.707 4.298 1 49.87 ? H5A1 PLP 501 A 1 HETATM 22 H H5A2 PLP . . . B 2 28.377 46.348 3.761 1 49.87 ? H5A2 PLP 501 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #