data_8DLE # _model_server_result.job_id SDSVwEmg6v4zVrXUt2KfOw _model_server_result.datetime_utc '2025-03-06 01:10:25' _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 8dle # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8DLE # _exptl.entry_id 8DLE _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 8DLE _cell.length_a 94.49 _cell.length_b 162.31 _cell.length_c 70.97 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DLE _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 _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 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 OH TYR 264 A TYR 264 1_555 I S8 SWC . B SWC 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.653 ? covale ? covale2 B OG SER 37 B SER 36 1_555 I P33 SWC . B SWC 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? # _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 269 n y N1 C6 PLP sing 270 n y C2 C2A PLP sing 271 n n C2 C3 PLP sing 272 n y C2A H2A1 PLP sing 273 n n C2A H2A2 PLP sing 274 n n C2A H2A3 PLP sing 275 n n C3 O3 PLP sing 276 n n C3 C4 PLP doub 277 n y O3 HO3 PLP sing 278 n n C4 C4A PLP sing 279 n n C4 C5 PLP sing 280 n y C4A O4A PLP doub 281 n n C4A H4A PLP sing 282 n n C5 C6 PLP doub 283 n y C5 C5A PLP sing 284 n n C6 H6 PLP sing 285 n n C5A O4P PLP sing 286 n n C5A H5A1 PLP sing 287 n n C5A H5A2 PLP sing 288 n n O4P P PLP sing 289 n n P O1P PLP doub 290 n n P O2P PLP sing 291 n n P O3P PLP sing 292 n n O2P HOP2 PLP sing 293 n n O3P HOP3 PLP sing 294 n n # _atom_sites.entry_id 8DLE _atom_sites.fract_transf_matrix[1][1] 0.010583 _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] 0.006161 _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] 0.01409 _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 C 3 PLP A 1 401 1 PLP PLP . D 4 EDO A 1 402 2 EDO EDO . E 4 EDO A 1 403 3 EDO EDO . F 5 SO4 A 1 404 3 SO4 SO4 . G 5 SO4 A 1 405 94 SO4 SO4 . H 5 SO4 A 1 406 95 SO4 SO4 . I 6 SWC B 1 101 1 SWC BSF . J 7 HOH A 1 501 48 HOH HOH . J 7 HOH A 2 502 82 HOH HOH . J 7 HOH A 3 503 4 HOH HOH . J 7 HOH A 4 504 7 HOH HOH . J 7 HOH A 5 505 64 HOH HOH . J 7 HOH A 6 506 13 HOH HOH . J 7 HOH A 7 507 10 HOH HOH . J 7 HOH A 8 508 51 HOH HOH . J 7 HOH A 9 509 31 HOH HOH . J 7 HOH A 10 510 35 HOH HOH . J 7 HOH A 11 511 37 HOH HOH . J 7 HOH A 12 512 57 HOH HOH . J 7 HOH A 13 513 22 HOH HOH . J 7 HOH A 14 514 71 HOH HOH . J 7 HOH A 15 515 42 HOH HOH . J 7 HOH A 16 516 83 HOH HOH . J 7 HOH A 17 517 29 HOH HOH . J 7 HOH A 18 518 52 HOH HOH . J 7 HOH A 19 519 55 HOH HOH . J 7 HOH A 20 520 39 HOH HOH . J 7 HOH A 21 521 8 HOH HOH . J 7 HOH A 22 522 32 HOH HOH . J 7 HOH A 23 523 30 HOH HOH . J 7 HOH A 24 524 61 HOH HOH . J 7 HOH A 25 525 38 HOH HOH . J 7 HOH A 26 526 16 HOH HOH . J 7 HOH A 27 527 1 HOH HOH . J 7 HOH A 28 528 2 HOH HOH . J 7 HOH A 29 529 27 HOH HOH . J 7 HOH A 30 530 15 HOH HOH . J 7 HOH A 31 531 65 HOH HOH . J 7 HOH A 32 532 23 HOH HOH . J 7 HOH A 33 533 56 HOH HOH . J 7 HOH A 34 534 3 HOH HOH . J 7 HOH A 35 535 59 HOH HOH . J 7 HOH A 36 536 5 HOH HOH . J 7 HOH A 37 537 40 HOH HOH . J 7 HOH A 38 538 6 HOH HOH . J 7 HOH A 39 539 54 HOH HOH . J 7 HOH A 40 540 62 HOH HOH . J 7 HOH A 41 541 9 HOH HOH . J 7 HOH A 42 542 33 HOH HOH . J 7 HOH A 43 543 34 HOH HOH . J 7 HOH A 44 544 11 HOH HOH . J 7 HOH A 45 545 25 HOH HOH . J 7 HOH A 46 546 63 HOH HOH . J 7 HOH A 47 547 28 HOH HOH . J 7 HOH A 48 548 24 HOH HOH . J 7 HOH A 49 549 26 HOH HOH . J 7 HOH A 50 550 58 HOH HOH . J 7 HOH A 51 551 66 HOH HOH . J 7 HOH A 52 552 75 HOH HOH . J 7 HOH A 53 553 60 HOH HOH . J 7 HOH A 54 554 46 HOH HOH . J 7 HOH A 55 555 18 HOH HOH . J 7 HOH A 56 556 92 HOH HOH . J 7 HOH A 57 557 43 HOH HOH . J 7 HOH A 58 558 68 HOH HOH . J 7 HOH A 59 559 41 HOH HOH . J 7 HOH A 60 560 50 HOH HOH . J 7 HOH A 61 561 21 HOH HOH . J 7 HOH A 62 562 20 HOH HOH . J 7 HOH A 63 563 86 HOH HOH . J 7 HOH A 64 564 88 HOH HOH . J 7 HOH A 65 565 84 HOH HOH . J 7 HOH A 66 566 47 HOH HOH . J 7 HOH A 67 567 14 HOH HOH . J 7 HOH A 68 568 80 HOH HOH . J 7 HOH A 69 569 19 HOH HOH . J 7 HOH A 70 570 89 HOH HOH . J 7 HOH A 71 571 87 HOH HOH . J 7 HOH A 72 572 70 HOH HOH . J 7 HOH A 73 573 44 HOH HOH . J 7 HOH A 74 574 78 HOH HOH . J 7 HOH A 75 575 93 HOH HOH . J 7 HOH A 76 576 67 HOH HOH . J 7 HOH A 77 577 79 HOH HOH . J 7 HOH A 78 578 91 HOH HOH . J 7 HOH A 79 579 17 HOH HOH . J 7 HOH A 80 580 85 HOH HOH . J 7 HOH A 81 581 72 HOH HOH . J 7 HOH A 82 582 69 HOH HOH . J 7 HOH A 83 583 49 HOH HOH . J 7 HOH A 84 584 90 HOH HOH . J 7 HOH A 85 585 81 HOH HOH . J 7 HOH A 86 586 73 HOH HOH . J 7 HOH A 87 587 74 HOH HOH . J 7 HOH A 88 588 76 HOH HOH . K 7 HOH B 1 201 36 HOH HOH . K 7 HOH B 2 202 45 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 5.896 25.428 -3.841 1 73.69 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . C 3 5.181 24.8 -4.836 1 75.18 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . C 3 3.829 25.315 -5.224 1 75.79 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . C 3 5.707 23.689 -5.482 1 86.16 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . C 3 4.984 23.077 -6.472 1 84.21 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . C 3 6.961 23.196 -5.135 1 90.81 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . C 3 7.63 22.256 -6.101 1 78.12 ? C4A PLP 401 A 1 HETATM 8 O O4A PLP . . . C 3 8.736 22.497 -6.585 1 68.63 ? O4A PLP 401 A 1 HETATM 9 C C5 PLP . . . C 3 7.678 23.839 -4.125 1 91.83 ? C5 PLP 401 A 1 HETATM 10 C C6 PLP . . . C 3 7.139 24.949 -3.486 1 82.29 ? C6 PLP 401 A 1 HETATM 11 C C5A PLP . . . C 3 9.045 23.361 -3.692 1 94.19 ? C5A PLP 401 A 1 HETATM 12 O O4P PLP . . . C 3 9.436 24.1 -2.558 1 104.14 ? O4P PLP 401 A 1 HETATM 13 P P PLP . . . C 3 10.543 25.261 -2.694 1 126.48 ? P PLP 401 A 1 HETATM 14 O O1P PLP . . . C 3 10.924 25.424 -4.146 1 111.2 ? O1P PLP 401 A 1 HETATM 15 O O2P PLP . . . C 3 11.755 24.875 -1.881 1 110.73 ? O2P PLP 401 A 1 HETATM 16 O O3P PLP . . . C 3 9.97 26.558 -2.172 1 96.81 ? O3P PLP 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 198 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 474 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 16 #