data_2DU9 # _model_server_result.job_id U7lo7pRaeoLIpZ7TY4qc2w _model_server_result.datetime_utc '2025-03-01 01:53:39' _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 2du9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":130}' # _entry.id 2DU9 # _exptl.entry_id 2DU9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 2DU9 _cell.length_a 46.95 _cell.length_b 46.95 _cell.length_c 152.48 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DU9 _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,PQS _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_775 -y+2,-x+2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 93.9 93.9 76.24 # _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 # 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 C GLY 65 A GLY 65 1_555 A N MSE 66 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 A C MSE 66 A MSE 66 1_555 A N PHE 67 A PHE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 C1 C2 MPD sing 224 n n C1 H11 MPD sing 225 n n C1 H12 MPD sing 226 n n C1 H13 MPD sing 227 n n C2 O2 MPD sing 228 n n C2 CM MPD sing 229 n n C2 C3 MPD sing 230 n n O2 HO2 MPD sing 231 n n CM HM1 MPD sing 232 n n CM HM2 MPD sing 233 n n CM HM3 MPD sing 234 n n C3 C4 MPD sing 235 n n C3 H31 MPD sing 236 n n C3 H32 MPD sing 237 n n C4 O4 MPD sing 238 n n C4 C5 MPD sing 239 n n C4 H4 MPD sing 240 n n O4 HO4 MPD sing 241 n n C5 H51 MPD sing 242 n n C5 H52 MPD sing 243 n n C5 H53 MPD sing 244 n n # _atom_sites.entry_id 2DU9 _atom_sites.fract_transf_matrix[1][1] 0.021299 _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] 0.021299 _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] 0.006558 _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 MPD A 1 130 101 MPD MPD . C 3 HOH A 1 131 1 HOH WAT . C 3 HOH A 2 132 2 HOH WAT . C 3 HOH A 3 133 3 HOH WAT . C 3 HOH A 4 134 4 HOH WAT . C 3 HOH A 5 135 5 HOH WAT . C 3 HOH A 6 136 6 HOH WAT . C 3 HOH A 7 137 7 HOH WAT . C 3 HOH A 8 138 8 HOH WAT . C 3 HOH A 9 139 9 HOH WAT . C 3 HOH A 10 140 10 HOH WAT . C 3 HOH A 11 141 11 HOH WAT . C 3 HOH A 12 142 12 HOH WAT . C 3 HOH A 13 143 13 HOH WAT . C 3 HOH A 14 144 14 HOH WAT . C 3 HOH A 15 145 15 HOH WAT . C 3 HOH A 16 146 16 HOH WAT . C 3 HOH A 17 147 17 HOH WAT . C 3 HOH A 18 148 18 HOH WAT . C 3 HOH A 19 149 19 HOH WAT . C 3 HOH A 20 150 20 HOH WAT . C 3 HOH A 21 151 21 HOH WAT . C 3 HOH A 22 152 22 HOH WAT . C 3 HOH A 23 153 23 HOH WAT . C 3 HOH A 24 154 24 HOH WAT . C 3 HOH A 25 155 25 HOH WAT . C 3 HOH A 26 156 26 HOH WAT . C 3 HOH A 27 157 27 HOH WAT . C 3 HOH A 28 158 28 HOH WAT . C 3 HOH A 29 159 29 HOH WAT . C 3 HOH A 30 160 30 HOH WAT . C 3 HOH A 31 161 31 HOH WAT . C 3 HOH A 32 162 32 HOH WAT . C 3 HOH A 33 163 33 HOH WAT . C 3 HOH A 34 164 34 HOH WAT . C 3 HOH A 35 165 35 HOH WAT . C 3 HOH A 36 166 36 HOH WAT . C 3 HOH A 37 167 37 HOH WAT . C 3 HOH A 38 168 38 HOH WAT . C 3 HOH A 39 169 39 HOH WAT . C 3 HOH A 40 170 40 HOH WAT . C 3 HOH A 41 171 41 HOH WAT . C 3 HOH A 42 172 42 HOH WAT . C 3 HOH A 43 173 43 HOH WAT . C 3 HOH A 44 174 44 HOH WAT . C 3 HOH A 45 175 45 HOH WAT . C 3 HOH A 46 176 46 HOH WAT . C 3 HOH A 47 177 47 HOH WAT . # 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 C1 MPD . . . B 2 47.836 44.557 28.41 1 59.91 ? C1 MPD 130 A 1 HETATM 2 C C2 MPD . . . B 2 48.939 44.937 29.28 1 60.22 ? C2 MPD 130 A 1 HETATM 3 O O2 MPD . . . B 2 50.103 44.277 28.598 1 58.54 ? O2 MPD 130 A 1 HETATM 4 C CM MPD . . . B 2 49.103 46.364 29.302 1 59.87 ? CM MPD 130 A 1 HETATM 5 C C3 MPD . . . B 2 48.386 44.52 30.688 1 61.43 ? C3 MPD 130 A 1 HETATM 6 C C4 MPD . . . B 2 48.476 42.954 30.796 1 62.77 ? C4 MPD 130 A 1 HETATM 7 O O4 MPD . . . B 2 49.912 42.604 31.482 1 64.86 ? O4 MPD 130 A 1 HETATM 8 C C5 MPD . . . B 2 47.737 42.509 31.962 1 64.5 ? C5 MPD 130 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 8 #