data_5OG0 # _model_server_result.job_id 82aiDcAagSLedWr5ofCaHQ _model_server_result.datetime_utc '2024-11-29 14:26:07' _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 5og0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5OG0 # _exptl.entry_id 5OG0 _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 5OG0 _cell.length_a 90.673 _cell.length_b 90.673 _cell.length_c 141.197 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OG0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 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 _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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -70.5985 # _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 209 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 209 _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 401 _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 1.49 _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 5OG0 _atom_sites.fract_transf_matrix[1][1] 0.011029 _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] 0.011029 _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] 0.007082 _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 1 401 1209 PLP PLP . C 3 HOH A 1 501 21 HOH HOH . C 3 HOH A 2 502 24 HOH HOH . C 3 HOH A 3 503 10 HOH HOH . C 3 HOH A 4 504 23 HOH HOH . C 3 HOH A 5 505 11 HOH HOH . C 3 HOH A 6 506 16 HOH HOH . C 3 HOH A 7 507 9 HOH HOH . C 3 HOH A 8 508 1 HOH HOH . C 3 HOH A 9 509 15 HOH HOH . C 3 HOH A 10 510 17 HOH HOH . C 3 HOH A 11 511 25 HOH HOH . C 3 HOH A 12 512 8 HOH HOH . C 3 HOH A 13 513 7 HOH HOH . C 3 HOH A 14 514 3 HOH HOH . C 3 HOH A 15 515 7 HOH HOH . C 3 HOH A 16 516 20 HOH HOH . C 3 HOH A 17 517 25 HOH HOH . C 3 HOH A 18 518 41 HOH HOH . C 3 HOH A 19 519 18 HOH HOH . C 3 HOH A 20 520 12 HOH HOH . C 3 HOH A 21 521 2 HOH HOH . C 3 HOH A 22 522 13 HOH HOH . C 3 HOH A 23 523 37 HOH HOH . C 3 HOH A 24 524 12 HOH HOH . C 3 HOH A 25 525 26 HOH HOH . C 3 HOH A 26 526 19 HOH HOH . C 3 HOH A 27 527 14 HOH HOH . C 3 HOH A 28 528 1 HOH HOH . C 3 HOH A 29 529 9 HOH HOH . C 3 HOH A 30 530 15 HOH HOH . C 3 HOH A 31 531 4 HOH HOH . C 3 HOH A 32 532 23 HOH HOH . C 3 HOH A 33 533 4 HOH HOH . C 3 HOH A 34 534 6 HOH HOH . C 3 HOH A 35 535 8 HOH HOH . C 3 HOH A 36 536 5 HOH HOH . C 3 HOH A 37 537 38 HOH HOH . C 3 HOH A 38 538 28 HOH HOH . C 3 HOH A 39 539 31 HOH HOH . C 3 HOH A 40 540 5 HOH HOH . C 3 HOH A 41 541 6 HOH HOH . C 3 HOH A 42 542 10 HOH HOH . C 3 HOH A 43 543 2 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 -13.686 9.087 -20.356 1 45.22 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . B 2 -14.626 9.442 -19.447 1 48.19 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . B 2 -14.246 9.635 -18.01 1 49.52 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . B 2 -16.064 9.656 -19.843 1 47.66 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . B 2 -17.033 10.014 -18.964 1 45.27 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . B 2 -16.449 9.479 -21.244 1 44.56 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . B 2 -17.917 9.702 -21.613 1 46.4 ? C4A PLP 401 A 1 HETATM 8 C C5 PLP . . . B 2 -15.306 9.097 -22.15 1 44.5 ? C5 PLP 401 A 1 HETATM 9 C C6 PLP . . . B 2 -13.999 8.915 -21.657 1 45.39 ? C6 PLP 401 A 1 HETATM 10 C C5A PLP . . . B 2 -15.54 8.827 -23.6 1 42.55 ? C5A PLP 401 A 1 HETATM 11 O O4P PLP . . . B 2 -15.626 10.02 -24.347 1 42.56 ? O4P PLP 401 A 1 HETATM 12 P P PLP . . . B 2 -16.216 9.856 -25.836 1 36.73 ? P PLP 401 A 1 HETATM 13 O O1P PLP . . . B 2 -15.087 9.293 -26.679 1 38.22 ? O1P PLP 401 A 1 HETATM 14 O O2P PLP . . . B 2 -16.434 11.331 -26.084 1 38.75 ? O2P PLP 401 A 1 HETATM 15 O O3P PLP . . . B 2 -17.353 8.881 -25.753 1 34.06 ? O3P PLP 401 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 15 #