data_8PK8 # _model_server_result.job_id o3xWyVjtq-R4GgKY_IWgJA _model_server_result.datetime_utc '2024-11-22 23:30:47' _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 8pk8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 8PK8 # _exptl.entry_id 8PK8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 247.142 _entity.id 6 _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 8PK8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PK8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 205 A LYS 258 1_555 F C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 C OG SER 37 C SER 37 1_555 G P24 8Q1 . C 8Q1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale3 D C HIS 105 D HIS 137 1_555 D N CSS 106 D CSS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 D C CSS 106 D CSS 138 1_555 D N SER 107 D SER 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 D OD1 ASP 39 D ASP 71 1_555 H FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc2 D OD2 ASP 39 D ASP 71 1_555 H FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc3 D SG CYS 63 D CYS 95 1_555 H FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 D SD CSS 106 D CSS 138 1_555 H FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc5 H FE FE2 . D FE2 201 1_555 L O HOH . D HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? # _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 353 n y N1 C6 PLP sing 354 n y C2 C2A PLP sing 355 n n C2 C3 PLP sing 356 n y C2A H2A1 PLP sing 357 n n C2A H2A2 PLP sing 358 n n C2A H2A3 PLP sing 359 n n C3 O3 PLP sing 360 n n C3 C4 PLP doub 361 n y O3 HO3 PLP sing 362 n n C4 C4A PLP sing 363 n n C4 C5 PLP sing 364 n y C4A O4A PLP doub 365 n n C4A H4A PLP sing 366 n n C5 C6 PLP doub 367 n y C5 C5A PLP sing 368 n n C6 H6 PLP sing 369 n n C5A O4P PLP sing 370 n n C5A H5A1 PLP sing 371 n n C5A H5A2 PLP sing 372 n n O4P P PLP sing 373 n n P O1P PLP doub 374 n n P O2P PLP sing 375 n n P O3P PLP sing 376 n n O2P HOP2 PLP sing 377 n n O3P HOP3 PLP sing 378 n n # _atom_sites.entry_id 8PK8 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 6 PLP A 1 501 501 PLP PLP . G 7 8Q1 C 1 101 101 8Q1 8Q1 . H 8 FE2 D 1 201 201 FE2 FE2 . I 9 HOH A 1 601 601 HOH HOH . I 9 HOH A 2 602 602 HOH HOH . I 9 HOH A 3 603 603 HOH HOH . I 9 HOH A 4 604 604 HOH HOH . I 9 HOH A 5 605 605 HOH HOH . I 9 HOH A 6 606 606 HOH HOH . I 9 HOH A 7 607 607 HOH HOH . I 9 HOH A 8 608 608 HOH HOH . I 9 HOH A 9 609 609 HOH HOH . I 9 HOH A 10 610 610 HOH HOH . I 9 HOH A 11 611 611 HOH HOH . I 9 HOH A 12 612 612 HOH HOH . I 9 HOH A 13 613 613 HOH HOH . I 9 HOH A 14 614 614 HOH HOH . I 9 HOH A 15 615 615 HOH HOH . I 9 HOH A 16 616 616 HOH HOH . I 9 HOH A 17 617 617 HOH HOH . I 9 HOH A 18 618 618 HOH HOH . I 9 HOH A 19 619 619 HOH HOH . I 9 HOH A 20 620 620 HOH HOH . I 9 HOH A 21 621 621 HOH HOH . I 9 HOH A 22 622 622 HOH HOH . I 9 HOH A 23 623 623 HOH HOH . I 9 HOH A 24 624 624 HOH HOH . I 9 HOH A 25 625 625 HOH HOH . I 9 HOH A 26 626 626 HOH HOH . I 9 HOH A 27 627 627 HOH HOH . I 9 HOH A 28 628 628 HOH HOH . I 9 HOH A 29 629 629 HOH HOH . I 9 HOH A 30 630 630 HOH HOH . I 9 HOH A 31 631 631 HOH HOH . I 9 HOH A 32 632 632 HOH HOH . I 9 HOH A 33 633 633 HOH HOH . I 9 HOH A 34 634 634 HOH HOH . I 9 HOH A 35 635 635 HOH HOH . I 9 HOH A 36 636 636 HOH HOH . I 9 HOH A 37 637 637 HOH HOH . I 9 HOH A 38 638 638 HOH HOH . I 9 HOH A 39 639 639 HOH HOH . I 9 HOH A 40 640 640 HOH HOH . I 9 HOH A 41 641 641 HOH HOH . I 9 HOH A 42 642 642 HOH HOH . I 9 HOH A 43 643 643 HOH HOH . I 9 HOH A 44 644 644 HOH HOH . I 9 HOH A 45 645 645 HOH HOH . I 9 HOH A 46 646 646 HOH HOH . I 9 HOH A 47 647 647 HOH HOH . I 9 HOH A 48 648 648 HOH HOH . I 9 HOH A 49 649 649 HOH HOH . I 9 HOH A 50 650 650 HOH HOH . I 9 HOH A 51 651 651 HOH HOH . I 9 HOH A 52 652 652 HOH HOH . I 9 HOH A 53 653 653 HOH HOH . I 9 HOH A 54 654 654 HOH HOH . I 9 HOH A 55 655 655 HOH HOH . I 9 HOH A 56 656 656 HOH HOH . I 9 HOH A 57 657 657 HOH HOH . I 9 HOH A 58 658 658 HOH HOH . I 9 HOH A 59 659 659 HOH HOH . I 9 HOH A 60 660 660 HOH HOH . I 9 HOH A 61 661 661 HOH HOH . I 9 HOH A 62 662 662 HOH HOH . I 9 HOH A 63 663 663 HOH HOH . I 9 HOH A 64 664 664 HOH HOH . I 9 HOH A 65 665 665 HOH HOH . I 9 HOH A 66 666 666 HOH HOH . I 9 HOH A 67 667 667 HOH HOH . I 9 HOH A 68 668 668 HOH HOH . I 9 HOH A 69 669 669 HOH HOH . I 9 HOH A 70 670 670 HOH HOH . I 9 HOH A 71 671 671 HOH HOH . I 9 HOH A 72 672 672 HOH HOH . I 9 HOH A 73 673 673 HOH HOH . I 9 HOH A 74 674 674 HOH HOH . I 9 HOH A 75 675 675 HOH HOH . I 9 HOH A 76 676 676 HOH HOH . I 9 HOH A 77 677 677 HOH HOH . I 9 HOH A 78 678 678 HOH HOH . I 9 HOH A 79 679 679 HOH HOH . I 9 HOH A 80 680 680 HOH HOH . I 9 HOH A 81 681 681 HOH HOH . I 9 HOH A 82 682 682 HOH HOH . I 9 HOH A 83 683 683 HOH HOH . I 9 HOH A 84 684 684 HOH HOH . I 9 HOH A 85 685 685 HOH HOH . I 9 HOH A 86 686 686 HOH HOH . I 9 HOH A 87 687 687 HOH HOH . I 9 HOH A 88 688 688 HOH HOH . I 9 HOH A 89 689 689 HOH HOH . I 9 HOH A 90 690 690 HOH HOH . I 9 HOH A 91 691 691 HOH HOH . I 9 HOH A 92 692 692 HOH HOH . I 9 HOH A 93 693 693 HOH HOH . I 9 HOH A 94 694 694 HOH HOH . I 9 HOH A 95 695 695 HOH HOH . I 9 HOH A 96 696 696 HOH HOH . I 9 HOH A 97 697 697 HOH HOH . I 9 HOH A 98 698 698 HOH HOH . I 9 HOH A 99 699 699 HOH HOH . I 9 HOH A 100 700 700 HOH HOH . J 9 HOH B 1 101 101 HOH HOH . J 9 HOH B 2 102 102 HOH HOH . J 9 HOH B 3 103 103 HOH HOH . J 9 HOH B 4 104 104 HOH HOH . J 9 HOH B 5 105 105 HOH HOH . J 9 HOH B 6 106 106 HOH HOH . J 9 HOH B 7 107 107 HOH HOH . J 9 HOH B 8 108 108 HOH HOH . J 9 HOH B 9 109 109 HOH HOH . J 9 HOH B 10 110 110 HOH HOH . J 9 HOH B 11 111 111 HOH HOH . J 9 HOH B 12 112 112 HOH HOH . J 9 HOH B 13 113 113 HOH HOH . J 9 HOH B 14 114 114 HOH HOH . J 9 HOH B 15 115 115 HOH HOH . J 9 HOH B 16 116 116 HOH HOH . J 9 HOH B 17 117 117 HOH HOH . J 9 HOH B 18 118 118 HOH HOH . K 9 HOH C 1 201 201 HOH HOH . L 9 HOH D 1 301 301 HOH HOH . L 9 HOH D 2 302 302 HOH HOH . L 9 HOH D 3 303 303 HOH HOH . L 9 HOH D 4 304 304 HOH HOH . L 9 HOH D 5 305 305 HOH HOH . L 9 HOH D 6 306 306 HOH HOH . L 9 HOH D 7 307 307 HOH HOH . L 9 HOH D 8 308 308 HOH HOH . L 9 HOH D 9 309 309 HOH HOH . L 9 HOH D 10 310 310 HOH HOH . L 9 HOH D 11 311 311 HOH HOH . L 9 HOH D 12 312 312 HOH HOH . L 9 HOH D 13 313 313 HOH HOH . L 9 HOH D 14 314 314 HOH HOH . L 9 HOH D 15 315 315 HOH HOH . L 9 HOH D 16 316 316 HOH HOH . M 9 HOH E 1 301 301 HOH HOH . M 9 HOH E 2 302 302 HOH HOH . M 9 HOH E 3 303 303 HOH HOH . M 9 HOH E 4 304 304 HOH HOH . M 9 HOH E 5 305 305 HOH HOH . M 9 HOH E 6 306 306 HOH HOH . M 9 HOH E 7 307 307 HOH HOH . M 9 HOH E 8 308 308 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 . . . F 6 99.999 117.954 113.695 1 18.96 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . F 6 99.184 118.649 112.908 1 18.96 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . F 6 98.8 120.034 113.308 1 18.96 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . F 6 98.693 118.095 111.723 1 18.96 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . F 6 97.862 118.843 110.963 1 18.96 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . F 6 99.068 116.788 111.362 1 18.96 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . F 6 98.557 116.205 110.122 1 18.96 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . F 6 99.932 116.083 112.211 1 18.96 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . F 6 100.364 116.702 113.35 1 18.96 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . F 6 100.38 114.684 111.897 1 18.96 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . F 6 101.539 114.706 111.006 1 18.96 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . F 6 102.027 113.379 110.233 1 18.96 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . F 6 103.176 113.81 109.348 1 18.96 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . F 6 102.448 112.397 111.304 1 18.96 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . F 6 100.824 112.914 109.447 1 18.96 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #