data_8P90 # _model_server_result.job_id uipGs5wgy8UIJexGS4Efrw _model_server_result.datetime_utc '2024-11-13 05:06:25' _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 8p90 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":409}' # _entry.id 8P90 # _exptl.entry_id 8P90 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 5 _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 120 _cell.entry_id 8P90 _cell.length_a 94.657 _cell.length_b 94.657 _cell.length_c 441.848 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8P90 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall 'P 65 2 (x,y,z+1/12)' _symmetry.space_group_name_H-M 'P 65 2 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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 5 _struct_asym.id K _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 metalc ? metalc1 A NE2 HIS 185 A HIS 185 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A ND1 HIS 187 A HIS 187 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc3 A OD2 ASP 189 A ASP 189 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? metalc ? metalc4 A NE2 HIS 190 A HIS 190 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc5 A NE2 HIS 253 A HIS 253 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc6 A OD2 ASP 284 A ASP 284 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc7 A OD2 ASP 284 A ASP 284 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc8 A NE2 HIS 343 A HIS 343 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc9 C ZN ZN . A ZN 401 1_555 E O12 3PE . A 3PE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc10 D ZN ZN . A ZN 402 1_555 E O14 3PE . A 3PE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc11 B NE2 HIS 185 B HIS 185 1_555 N ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc12 B ND1 HIS 187 B HIS 187 1_555 N ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc13 B OD2 ASP 189 B ASP 189 1_555 O ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc14 B NE2 HIS 190 B HIS 190 1_555 O ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc15 B NE2 HIS 253 B HIS 253 1_555 N ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc16 B OD2 ASP 284 B ASP 284 1_555 O ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc17 B NE2 HIS 343 B HIS 343 1_555 O ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc18 N ZN ZN . B ZN 603 1_555 P O12 3PE . B 3PE 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc19 O ZN ZN . B ZN 604 1_555 P O14 3PE . B 3PE 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? # _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 463 n y N1 C6 PLP sing 464 n y C2 C2A PLP sing 465 n n C2 C3 PLP sing 466 n y C2A H2A1 PLP sing 467 n n C2A H2A2 PLP sing 468 n n C2A H2A3 PLP sing 469 n n C3 O3 PLP sing 470 n n C3 C4 PLP doub 471 n y O3 HO3 PLP sing 472 n n C4 C4A PLP sing 473 n n C4 C5 PLP sing 474 n y C4A O4A PLP doub 475 n n C4A H4A PLP sing 476 n n C5 C6 PLP doub 477 n y C5 C5A PLP sing 478 n n C6 H6 PLP sing 479 n n C5A O4P PLP sing 480 n n C5A H5A1 PLP sing 481 n n C5A H5A2 PLP sing 482 n n O4P P PLP sing 483 n n P O1P PLP doub 484 n n P O2P PLP sing 485 n n P O3P PLP sing 486 n n O2P HOP2 PLP sing 487 n n O3P HOP3 PLP sing 488 n n # _atom_sites.entry_id 8P90 _atom_sites.fract_transf_matrix[1][1] 0.010564 _atom_sites.fract_transf_matrix[1][2] 0.006099 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012199 _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] 0.002263 _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 2 ZN A 1 401 401 ZN ZN . D 2 ZN A 1 402 402 ZN ZN . E 3 3PE A 1 403 503 3PE 3PE . F 4 DXC A 1 404 602 DXC DXC . G 4 DXC A 1 405 603 DXC DXC . H 4 DXC A 1 406 605 DXC DXC . I 4 DXC A 1 407 601 DXC DXC . J 4 DXC A 1 408 604 DXC DXC . K 5 PLP A 1 409 100 PLP PLP . L 4 DXC B 1 601 601 DXC DXC . M 4 DXC B 1 602 604 DXC DXC . N 2 ZN B 1 603 401 ZN ZN . O 2 ZN B 1 604 402 ZN ZN . P 3 3PE B 1 605 503 3PE 3PE . Q 4 DXC B 1 606 602 DXC DXC . R 4 DXC B 1 607 603 DXC DXC . S 4 DXC B 1 608 605 DXC DXC . T 6 HOH A 1 501 21 HOH HOH . T 6 HOH A 2 502 17 HOH HOH . T 6 HOH A 3 503 11 HOH HOH . T 6 HOH A 4 504 1 HOH HOH . T 6 HOH A 5 505 16 HOH HOH . T 6 HOH A 6 506 27 HOH HOH . T 6 HOH A 7 507 2 HOH HOH . T 6 HOH A 8 508 7 HOH HOH . T 6 HOH A 9 509 24 HOH HOH . T 6 HOH A 10 510 12 HOH HOH . T 6 HOH A 11 511 3 HOH HOH . T 6 HOH A 12 512 10 HOH HOH . T 6 HOH A 13 513 6 HOH HOH . U 6 HOH B 1 701 23 HOH HOH . U 6 HOH B 2 702 13 HOH HOH . U 6 HOH B 3 703 22 HOH HOH . U 6 HOH B 4 704 15 HOH HOH . U 6 HOH B 5 705 26 HOH HOH . U 6 HOH B 6 706 29 HOH HOH . U 6 HOH B 7 707 4 HOH HOH . U 6 HOH B 8 708 5 HOH HOH . U 6 HOH B 9 709 14 HOH HOH . U 6 HOH B 10 710 18 HOH HOH . U 6 HOH B 11 711 20 HOH HOH . U 6 HOH B 12 712 28 HOH HOH . U 6 HOH B 13 713 9 HOH HOH . U 6 HOH B 14 714 19 HOH HOH . U 6 HOH B 15 715 30 HOH HOH . U 6 HOH B 16 716 25 HOH HOH . U 6 HOH B 17 717 8 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 . . . K 5 -1.998 24.063 186.906 1 128.31 ? N1 PLP 409 A 1 HETATM 2 C C2 PLP . . . K 5 -1.331 25.251 186.689 1 128.58 ? C2 PLP 409 A 1 HETATM 3 C C2A PLP . . . K 5 0.129 25.243 186.347 1 128.89 ? C2A PLP 409 A 1 HETATM 4 C C3 PLP . . . K 5 -1.873 26.438 186.861 1 128.76 ? C3 PLP 409 A 1 HETATM 5 O O3 PLP . . . K 5 -1.14 27.57 186.75 1 129.19 ? O3 PLP 409 A 1 HETATM 6 C C4 PLP . . . K 5 -3.234 26.456 187.178 1 128.65 ? C4 PLP 409 A 1 HETATM 7 C C4A PLP . . . K 5 -4.15 27.73 187.45 1 129 ? C4A PLP 409 A 1 HETATM 8 O O4A PLP . . . K 5 -3.53 28.84 187.28 1 129.42 ? O4A PLP 409 A 1 HETATM 9 C C5 PLP . . . K 5 -4.035 25.267 187.322 1 128.37 ? C5 PLP 409 A 1 HETATM 10 C C6 PLP . . . K 5 -3.343 24.065 187.217 1 128.21 ? C6 PLP 409 A 1 HETATM 11 C C5A PLP . . . K 5 -5.512 25.257 187.655 1 128.44 ? C5A PLP 409 A 1 HETATM 12 O O4P PLP . . . K 5 -5.743 24.722 188.941 1 128.38 ? O4P PLP 409 A 1 HETATM 13 P P PLP . . . K 5 -6.959 23.695 189.213 1 128.49 ? P PLP 409 A 1 HETATM 14 O O1P PLP . . . K 5 -7.026 22.678 188.097 1 128.42 -1 O1P PLP 409 A 1 HETATM 15 O O2P PLP . . . K 5 -6.688 22.974 190.514 1 128.49 ? O2P PLP 409 A 1 HETATM 16 O O3P PLP . . . K 5 -8.269 24.444 189.292 1 128.87 ? O3P PLP 409 A 1 # _model_server_stats.io_time_ms 112 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 16 #