data_1IX8 # _model_server_result.job_id J4BkgR2CvqNou6ZJlC3Fsw _model_server_result.datetime_utc '2024-10-21 02:34:56' _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 1ix8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":413}' # _entry.id 1IX8 # _exptl.entry_id 1IX8 _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 1IX8 _cell.length_a 154.973 _cell.length_b 88.739 _cell.length_c 80.298 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IX8 _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' 4_555 x,-y,-z 1 0 0 0 -1 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 246 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 258 _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 413 _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 1.366 _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 1IX8 _atom_sites.fract_transf_matrix[1][1] 0.006453 _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] 0.011269 _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] 0.012454 _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 1 413 413 PLP PLP . C 3 HOH A 1 501 501 HOH HOH . C 3 HOH A 2 502 502 HOH HOH . C 3 HOH A 3 503 503 HOH HOH . C 3 HOH A 4 504 504 HOH HOH . C 3 HOH A 5 505 505 HOH HOH . C 3 HOH A 6 506 506 HOH HOH . C 3 HOH A 7 507 507 HOH HOH . C 3 HOH A 8 508 508 HOH HOH . C 3 HOH A 9 509 509 HOH HOH . C 3 HOH A 10 510 510 HOH HOH . C 3 HOH A 11 511 511 HOH HOH . C 3 HOH A 12 512 512 HOH HOH . C 3 HOH A 13 513 513 HOH HOH . C 3 HOH A 14 514 514 HOH HOH . C 3 HOH A 15 515 515 HOH HOH . C 3 HOH A 16 516 516 HOH HOH . C 3 HOH A 17 517 517 HOH HOH . C 3 HOH A 18 518 518 HOH HOH . C 3 HOH A 19 519 519 HOH HOH . C 3 HOH A 20 520 520 HOH HOH . C 3 HOH A 21 521 521 HOH HOH . C 3 HOH A 22 522 522 HOH HOH . C 3 HOH A 23 523 523 HOH HOH . C 3 HOH A 24 524 524 HOH HOH . C 3 HOH A 25 525 525 HOH HOH . C 3 HOH A 26 526 526 HOH HOH . C 3 HOH A 27 527 527 HOH HOH . C 3 HOH A 28 528 528 HOH HOH . C 3 HOH A 29 529 529 HOH HOH . C 3 HOH A 30 530 530 HOH HOH . C 3 HOH A 31 531 531 HOH HOH . C 3 HOH A 32 532 532 HOH HOH . C 3 HOH A 33 533 533 HOH HOH . C 3 HOH A 34 534 534 HOH HOH . C 3 HOH A 35 535 535 HOH HOH . C 3 HOH A 36 536 536 HOH HOH . C 3 HOH A 37 537 537 HOH HOH . C 3 HOH A 38 538 538 HOH HOH . C 3 HOH A 39 539 539 HOH HOH . C 3 HOH A 40 540 540 HOH HOH . C 3 HOH A 41 541 541 HOH HOH . C 3 HOH A 42 542 542 HOH HOH . C 3 HOH A 43 543 543 HOH HOH . C 3 HOH A 44 544 544 HOH HOH . C 3 HOH A 45 545 545 HOH HOH . C 3 HOH A 46 546 546 HOH HOH . C 3 HOH A 47 547 547 HOH HOH . C 3 HOH A 48 548 548 HOH HOH . C 3 HOH A 49 549 549 HOH HOH . C 3 HOH A 50 550 550 HOH HOH . C 3 HOH A 51 551 551 HOH HOH . C 3 HOH A 52 552 552 HOH HOH . C 3 HOH A 53 553 553 HOH HOH . C 3 HOH A 54 554 554 HOH HOH . C 3 HOH A 55 555 555 HOH HOH . C 3 HOH A 56 556 556 HOH HOH . C 3 HOH A 57 557 557 HOH HOH . C 3 HOH A 58 558 558 HOH HOH . C 3 HOH A 59 559 559 HOH HOH . C 3 HOH A 60 560 560 HOH HOH . C 3 HOH A 61 561 561 HOH HOH . C 3 HOH A 62 562 562 HOH HOH . C 3 HOH A 63 563 563 HOH HOH . C 3 HOH A 64 564 564 HOH HOH . C 3 HOH A 65 565 565 HOH HOH . C 3 HOH A 66 566 566 HOH HOH . C 3 HOH A 67 567 567 HOH HOH . C 3 HOH A 68 568 568 HOH HOH . C 3 HOH A 69 569 569 HOH HOH . C 3 HOH A 70 570 570 HOH HOH . C 3 HOH A 71 571 571 HOH HOH . C 3 HOH A 72 572 572 HOH HOH . C 3 HOH A 73 573 573 HOH HOH . C 3 HOH A 74 574 574 HOH HOH . C 3 HOH A 75 575 575 HOH HOH . C 3 HOH A 76 576 576 HOH HOH . C 3 HOH A 77 577 577 HOH HOH . C 3 HOH A 78 578 578 HOH HOH . C 3 HOH A 79 579 579 HOH HOH . C 3 HOH A 80 580 580 HOH HOH . C 3 HOH A 81 581 581 HOH HOH . C 3 HOH A 82 582 582 HOH HOH . C 3 HOH A 83 583 583 HOH HOH . C 3 HOH A 84 584 584 HOH HOH . C 3 HOH A 85 585 585 HOH HOH . C 3 HOH A 86 586 586 HOH HOH . C 3 HOH A 87 587 587 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 26.723 5.308 -14.469 1 12.72 ? N1 PLP 413 A 1 HETATM 2 C C2 PLP . . . B 2 26.04 6.167 -15.274 1 12.77 ? C2 PLP 413 A 1 HETATM 3 C C2A PLP . . . B 2 26.608 6.534 -16.651 1 12.84 ? C2A PLP 413 A 1 HETATM 4 C C3 PLP . . . B 2 24.86 6.699 -14.866 1 12.64 ? C3 PLP 413 A 1 HETATM 5 O O3 PLP . . . B 2 24.199 7.571 -15.71 1 12.91 ? O3 PLP 413 A 1 HETATM 6 C C4 PLP . . . B 2 24.338 6.376 -13.626 1 12.51 ? C4 PLP 413 A 1 HETATM 7 C C4A PLP . . . B 2 22.992 6.994 -13.215 1 12.38 ? C4A PLP 413 A 1 HETATM 8 C C5 PLP . . . B 2 25.045 5.491 -12.802 1 12.42 ? C5 PLP 413 A 1 HETATM 9 C C6 PLP . . . B 2 26.24 4.969 -13.245 1 12.62 ? C6 PLP 413 A 1 HETATM 10 C C5A PLP . . . B 2 24.605 5.059 -11.403 1 12.12 ? C5A PLP 413 A 1 HETATM 11 O O4P PLP . . . B 2 23.335 5.262 -11.04 1 11.66 ? O4P PLP 413 A 1 HETATM 12 P P PLP . . . B 2 22.608 4.756 -9.688 1 11.28 ? P PLP 413 A 1 HETATM 13 O O1P PLP . . . B 2 21.872 3.559 -10.086 1 11.51 ? O1P PLP 413 A 1 HETATM 14 O O2P PLP . . . B 2 21.905 5.99 -9.55 1 11.41 ? O2P PLP 413 A 1 HETATM 15 O O3P PLP . . . B 2 23.639 4.589 -8.641 1 11.55 ? O3P PLP 413 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #