data_3LVL # _model_server_result.job_id 1sO8PF1lW6oR0n8odUBlLg _model_server_result.datetime_utc '2024-11-30 16:46:09' _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 3lvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":764}' # _entry.id 3LVL # _exptl.entry_id 3LVL _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 120 _cell.entry_id 3LVL _cell.length_a 77.647 _cell.length_b 77.647 _cell.length_c 355.986 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 # _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 225 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 206 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _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 B _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 764 _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 1.646 _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 3LVL _atom_sites.fract_transf_matrix[1][1] 0.012879 _atom_sites.fract_transf_matrix[1][2] 0.007436 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014871 _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] 0.002809 _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 B 1 764 764 PLP PLP . D 4 HOH B 1 405 1 HOH HOH . D 4 HOH B 2 406 2 HOH HOH . D 4 HOH B 3 407 3 HOH HOH . D 4 HOH B 4 408 4 HOH HOH . D 4 HOH B 5 409 6 HOH HOH . D 4 HOH B 6 410 8 HOH HOH . D 4 HOH B 7 411 9 HOH HOH . D 4 HOH B 8 412 10 HOH HOH . D 4 HOH B 9 413 13 HOH HOH . D 4 HOH B 10 414 19 HOH HOH . D 4 HOH B 11 415 21 HOH HOH . D 4 HOH B 12 416 22 HOH HOH . E 4 HOH A 1 129 7 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 -33.097 13.618 -4.81 1 60.62 ? N1 PLP 764 B 1 HETATM 2 C C2 PLP . . . C 3 -33.95 14.669 -4.889 1 60.62 ? C2 PLP 764 B 1 HETATM 3 C C2A PLP . . . C 3 -33.615 15.737 -5.877 1 60.62 ? C2A PLP 764 B 1 HETATM 4 C C3 PLP . . . C 3 -35.09 14.76 -4.077 1 60.62 ? C3 PLP 764 B 1 HETATM 5 O O3 PLP . . . C 3 -35.905 15.855 -4.215 1 60.62 ? O3 PLP 764 B 1 HETATM 6 C C4 PLP . . . C 3 -35.374 13.748 -3.155 1 60.62 ? C4 PLP 764 B 1 HETATM 7 C C4A PLP . . . C 3 -36.563 13.797 -2.278 1 60.62 ? C4A PLP 764 B 1 HETATM 8 C C5 PLP . . . C 3 -34.501 12.662 -3.071 1 60.62 ? C5 PLP 764 B 1 HETATM 9 C C6 PLP . . . C 3 -33.388 12.66 -3.919 1 60.62 ? C6 PLP 764 B 1 HETATM 10 C C5A PLP . . . C 3 -34.704 11.48 -2.107 1 60.62 ? C5A PLP 764 B 1 HETATM 11 O O4P PLP . . . C 3 -35.204 10.423 -2.775 1 60.62 ? O4P PLP 764 B 1 HETATM 12 P P PLP . . . C 3 -36.419 9.336 -1.892 1 60.62 ? P PLP 764 B 1 HETATM 13 O O1P PLP . . . C 3 -37.043 8.535 -2.993 1 60.62 ? O1P PLP 764 B 1 HETATM 14 O O2P PLP . . . C 3 -37.259 10.368 -1.199 1 60.62 ? O2P PLP 764 B 1 HETATM 15 O O3P PLP . . . C 3 -35.447 8.59 -0.979 1 60.62 ? O3P PLP 764 B 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #