data_6D7X # _model_server_result.job_id wX27XS-wYXrwawCIsqIRVg _model_server_result.datetime_utc '2024-10-20 01:29:54' _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 6d7x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":704}' # _entry.id 6D7X # _exptl.entry_id 6D7X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 214.262 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID' _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 6D7X _cell.length_a 144.35 _cell.length_b 144.35 _cell.length_c 113.37 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D7X _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 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 1,2,3,4 # 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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -144.35 0 3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -72.175 -72.175 0 4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 72.175 -72.175 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 covale ? covale1 A CD1 LEU 88 A LEU 88 1_555 E O DTB . A DTB 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale2 A OH TYR 115 A TYR 115 1_555 E CE DTB . A DTB 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale3 A O GLY 421 A GLY 421 1_555 D C12 FYY . A FYY 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? metalc ? metalc1 A OD1 ASP 541 A ASP 541 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc2 A OD1 ASP 541 A ASP 541 1_555 B CA CA . A CA 701 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? # _chem_comp.formula 'C10 H18 N2 O3' _chem_comp.formula_weight 214.262 _chem_comp.id DTB _chem_comp.mon_nstd_flag . _chem_comp.name '6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms D-DESTHIOBIOTIN # 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 CN O DTB doub 83 n n CN N2 DTB sing 84 n n CN N1 DTB sing 85 n n N2 CR DTB sing 86 n n N2 HN2 DTB sing 87 n n CR CS DTB sing 88 n n CR CE DTB sing 89 n n CR HCR DTB sing 90 n n CS N1 DTB sing 91 n n CS CT DTB sing 92 n n CS HCS DTB sing 93 n n N1 HN1 DTB sing 94 n n CT HCT1 DTB sing 95 n n CT HCT2 DTB sing 96 n n CT HCT3 DTB sing 97 n n CE CD DTB sing 98 n n CE HCE1 DTB sing 99 n n CE HCE2 DTB sing 100 n n CD CG DTB sing 101 n n CD HCD1 DTB sing 102 n n CD HCD2 DTB sing 103 n n CG CB DTB sing 104 n n CG HCG1 DTB sing 105 n n CG HCG2 DTB sing 106 n n CB CA DTB sing 107 n n CB HCB1 DTB sing 108 n n CB HCB2 DTB sing 109 n n CA C DTB sing 110 n n CA HCA1 DTB sing 111 n n CA HCA2 DTB sing 112 n n C OI1 DTB doub 113 n n C OI2 DTB sing 114 n n OI2 HOI2 DTB sing 115 n n # _atom_sites.entry_id 6D7X _atom_sites.fract_transf_matrix[1][1] 0.006928 _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] 0.006928 _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] 0.008821 _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 CA A 1 701 1 CA CA . C 2 CA A 1 702 2 CA CA . D 3 FYY A 1 703 1 FYY APB . E 4 DTB A 1 704 1 DTB DTB . # 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 CN DTB . . . E 4 40.185 -52.353 34.919 1 30.91 ? CN DTB 704 A 1 HETATM 2 O O DTB . . . E 4 40.196 -52.254 36.331 1 30.91 ? O DTB 704 A 1 HETATM 3 N N2 DTB . . . E 4 39.107 -52.385 34.129 1 30.91 ? N2 DTB 704 A 1 HETATM 4 C CR DTB . . . E 4 39.499 -52.492 32.872 1 30.91 ? CR DTB 704 A 1 HETATM 5 C CS DTB . . . E 4 40.896 -52.516 32.891 1 30.91 ? CS DTB 704 A 1 HETATM 6 N N1 DTB . . . E 4 41.277 -52.43 34.165 1 30.91 ? N1 DTB 704 A 1 HETATM 7 C CT DTB . . . E 4 41.807 -52.623 31.672 1 30.91 ? CT DTB 704 A 1 HETATM 8 C CE DTB . . . E 4 38.518 -52.552 31.689 1 30.91 ? CE DTB 704 A 1 HETATM 9 C CD DTB . . . E 4 37.074 -52.713 32.21 1 30.91 ? CD DTB 704 A 1 HETATM 10 C CG DTB . . . E 4 36.025 -53.103 31.157 1 30.91 ? CG DTB 704 A 1 HETATM 11 C CB DTB . . . E 4 35.231 -51.963 30.502 1 30.91 ? CB DTB 704 A 1 HETATM 12 C CA DTB . . . E 4 34.835 -52.326 29.057 1 30.91 ? CA DTB 704 A 1 HETATM 13 C C DTB . . . E 4 33.574 -51.614 28.517 1 30.91 ? C DTB 704 A 1 HETATM 14 O OI1 DTB . . . E 4 33.189 -51.796 27.311 1 30.91 ? OI1 DTB 704 A 1 HETATM 15 O OI2 DTB . . . E 4 32.904 -50.847 29.284 1 30.91 ? OI2 DTB 704 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #