data_3HKD # _model_server_result.job_id ZAj3CjmkVIKhdp3KJxVrPw _model_server_result.datetime_utc '2024-11-24 23:15:50' _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 3hkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":700}' # _entry.id 3HKD # _exptl.entry_id 3HKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.358 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3Z,5S)-5-benzyl-3-[1-(phenylamino)ethylidene]pyrrolidine-2,4-dione _entity.pdbx_number_of_molecules 2 _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 3HKD _cell.length_a 328.53 _cell.length_b 328.53 _cell.length_c 54.41 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 J N N ? 7 N N N # _chem_comp.formula 'C19 H18 N2 O2' _chem_comp.formula_weight 306.358 _chem_comp.id N16 _chem_comp.mon_nstd_flag . _chem_comp.name (3Z,5S)-5-benzyl-3-[1-(phenylamino)ethylidene]pyrrolidine-2,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 CAI CAM N16 doub 330 n y CAI CAE N16 sing 331 n y CAM CAV N16 sing 332 n y CAE CAH N16 doub 333 n y CAV NAO N16 sing 334 n n CAV CAL N16 doub 335 n y NAO CAQ N16 sing 336 n n OAB CAR N16 doub 337 n n CAH CAL N16 sing 338 n y CAQ CAA N16 sing 339 n n CAQ CAT N16 doub 340 n n CAR CAT N16 sing 341 n n CAR N N16 sing 342 n n CAT C N16 sing 343 n n N CA N16 sing 344 n n C CA N16 sing 345 n n C O N16 doub 346 n n CA CB N16 sing 347 n n CB CG N16 sing 348 n n CD2 CG N16 doub 349 n y CD2 CE2 N16 sing 350 n y CG CD1 N16 sing 351 n y CD1 CE1 N16 doub 352 n y CE2 CZ N16 doub 353 n y CZ CE1 N16 sing 354 n y CD1 HD1 N16 sing 355 z n CE1 HE1 N16 sing 356 n n CZ HZ N16 sing 357 n n CE2 HE2 N16 sing 358 n n CD2 HD2 N16 sing 359 n n CB HB N16 sing 360 n n CB HBA N16 sing 361 n n CA HA N16 sing 362 n n N HN N16 sing 363 n n CAA HAA N16 sing 364 n n CAA HAAA N16 sing 365 n n CAA HAAB N16 sing 366 n n NAO HNAO N16 sing 367 n n CAL HAL N16 sing 368 n n CAH HAH N16 sing 369 n n CAE HAE N16 sing 370 n n CAI HAI N16 sing 371 n n CAM HAM N16 sing 372 n n # _atom_sites.entry_id 3HKD _atom_sites.fract_transf_matrix[1][1] 0.003044 _atom_sites.fract_transf_matrix[1][2] 0.001757 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003515 _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] 0.018379 _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 F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 600 600 GDP GDP . I 5 MG B 1 601 601 MG MG . J 7 N16 B 1 700 700 N16 N16 . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 600 600 GDP GDP . N 7 N16 D 1 700 700 N16 N16 . # 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 C CD1 N16 . . . N 7 34.327 47.042 -4.284 1 80.41 ? CD1 N16 700 D 1 HETATM 2 C CE1 N16 . . . N 7 33.349 46.13 -3.853 1 79.6 ? CE1 N16 700 D 1 HETATM 3 C CZ N16 . . . N 7 32.017 46.239 -4.333 1 79.96 ? CZ N16 700 D 1 HETATM 4 C CE2 N16 . . . N 7 31.642 47.252 -5.241 1 79.53 ? CE2 N16 700 D 1 HETATM 5 C CD2 N16 . . . N 7 32.637 48.158 -5.676 1 81.49 ? CD2 N16 700 D 1 HETATM 6 C CG N16 . . . N 7 33.993 48.063 -5.209 1 83.24 ? CG N16 700 D 1 HETATM 7 C CB N16 . . . N 7 35.149 49.072 -5.66 1 84.58 ? CB N16 700 D 1 HETATM 8 C CA N16 . . . N 7 34.993 49.799 -7.058 1 84.97 ? CA N16 700 D 1 HETATM 9 C C N16 . . . N 7 36.005 50.984 -7.156 1 84.96 ? C N16 700 D 1 HETATM 10 O O N16 . . . N 7 36.036 52.039 -6.5 1 84.96 ? O N16 700 D 1 HETATM 11 N N N16 . . . N 7 35.476 48.872 -8.099 1 85.22 ? N N16 700 D 1 HETATM 12 C CAR N16 . . . N 7 36.594 49.363 -8.649 1 85.24 ? CAR N16 700 D 1 HETATM 13 O OAB N16 . . . N 7 37.203 48.752 -9.536 1 85.74 ? OAB N16 700 D 1 HETATM 14 C CAT N16 . . . N 7 36.932 50.63 -8.123 1 84.89 ? CAT N16 700 D 1 HETATM 15 C CAQ N16 . . . N 7 38.038 51.397 -8.5 1 83.96 ? CAQ N16 700 D 1 HETATM 16 C CAA N16 . . . N 7 38.376 52.794 -7.913 1 82.24 ? CAA N16 700 D 1 HETATM 17 N NAO N16 . . . N 7 38.764 50.843 -9.46 1 83.75 ? NAO N16 700 D 1 HETATM 18 C CAV N16 . . . N 7 39.896 51.287 -9.997 1 83.08 ? CAV N16 700 D 1 HETATM 19 C CAL N16 . . . N 7 40.976 51.47 -9.089 1 80.43 ? CAL N16 700 D 1 HETATM 20 C CAH N16 . . . N 7 42.224 51.898 -9.541 1 79.75 ? CAH N16 700 D 1 HETATM 21 C CAE N16 . . . N 7 42.38 52.091 -10.922 1 81.6 ? CAE N16 700 D 1 HETATM 22 C CAI N16 . . . N 7 41.309 51.889 -11.845 1 83.15 ? CAI N16 700 D 1 HETATM 23 C CAM N16 . . . N 7 40.039 51.467 -11.396 1 83.33 ? CAM N16 700 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #