data_3GP6 # _model_server_result.job_id gRzTM7V7YC5CwMRdMHr6GA _model_server_result.datetime_utc '2025-04-07 09:00:52' _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 3gp6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":174}' # _entry.id 3GP6 # _exptl.entry_id 3GP6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 9 _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 3GP6 _cell.length_a 113.228 _cell.length_b 113.228 _cell.length_c 55.064 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GP6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N 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 metalc ? metalc1 A O GLU 22 A GLU 21 1_555 X LI LI . A LI 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc2 A OXT LEU 163 A LEU 162 1_555 X LI LI . A LI 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? metalc ? metalc3 J O4 MPD . A MPD 171 1_555 X LI LI . A LI 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc4 Y LI LI . A LI 186 1_555 Z O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc5 Y LI LI . A LI 186 1_555 Z O HOH . A HOH 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? # _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 3GP6 _atom_sites.fract_transf_matrix[1][1] 0.008832 _atom_sites.fract_transf_matrix[1][2] 0.005099 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010198 _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] 0.018161 _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 SDS A 1 163 1 SDS SDS . C 2 SDS A 1 164 2 SDS SDS . D 2 SDS A 1 165 3 SDS SDS . E 2 SDS A 1 166 4 SDS SDS . F 2 SDS A 1 167 5 SDS SDS . G 2 SDS A 1 168 6 SDS SDS . H 3 MPD A 1 169 1 MPD MPD . I 3 MPD A 1 170 2 MPD MPD . J 3 MPD A 1 171 3 MPD MPD . K 3 MPD A 1 172 4 MPD MPD . L 3 MPD A 1 173 5 MPD MPD . M 3 MPD A 1 174 6 MPD MPD . N 3 MPD A 1 175 7 MPD MPD . O 3 MPD A 1 176 8 MPD MPD . P 3 MPD A 1 177 9 MPD MPD . Q 4 MRD A 1 178 10 MRD MPD . R 5 SO4 A 1 179 1 SO4 SO4 . S 5 SO4 A 1 180 2 SO4 SO4 . T 5 SO4 A 1 181 3 SO4 SO4 . U 5 SO4 A 1 182 4 SO4 SO4 . V 5 SO4 A 1 183 5 SO4 SO4 . W 5 SO4 A 1 184 6 SO4 SO4 . X 6 LI A 1 185 1 LI LI . Y 6 LI A 1 186 2 LI LI . Z 7 HOH A 1 187 1 HOH HOH . Z 7 HOH A 2 188 2 HOH HOH . Z 7 HOH A 3 189 3 HOH HOH . Z 7 HOH A 4 190 4 HOH HOH . Z 7 HOH A 5 191 5 HOH HOH . Z 7 HOH A 6 192 6 HOH HOH . Z 7 HOH A 7 193 7 HOH HOH . Z 7 HOH A 8 194 8 HOH HOH . Z 7 HOH A 9 195 9 HOH HOH . Z 7 HOH A 10 196 10 HOH HOH . Z 7 HOH A 11 197 11 HOH HOH . Z 7 HOH A 12 198 12 HOH HOH . Z 7 HOH A 13 199 13 HOH HOH . Z 7 HOH A 14 200 14 HOH HOH . Z 7 HOH A 15 201 15 HOH HOH . Z 7 HOH A 16 202 16 HOH HOH . Z 7 HOH A 17 203 17 HOH HOH . Z 7 HOH A 18 204 18 HOH HOH . Z 7 HOH A 19 205 19 HOH HOH . Z 7 HOH A 20 206 20 HOH HOH . Z 7 HOH A 21 207 21 HOH HOH . Z 7 HOH A 22 208 22 HOH HOH . Z 7 HOH A 23 209 23 HOH HOH . Z 7 HOH A 24 210 24 HOH HOH . Z 7 HOH A 25 211 25 HOH HOH . Z 7 HOH A 26 212 26 HOH HOH . Z 7 HOH A 27 213 27 HOH HOH . Z 7 HOH A 28 214 28 HOH HOH . Z 7 HOH A 29 215 29 HOH HOH . Z 7 HOH A 30 216 30 HOH HOH . Z 7 HOH A 31 217 31 HOH HOH . Z 7 HOH A 32 218 32 HOH HOH . Z 7 HOH A 33 219 33 HOH HOH . Z 7 HOH A 34 220 34 HOH HOH . Z 7 HOH A 35 221 35 HOH HOH . Z 7 HOH A 36 222 36 HOH HOH . Z 7 HOH A 37 223 37 HOH HOH . Z 7 HOH A 38 224 38 HOH HOH . Z 7 HOH A 39 225 39 HOH HOH . Z 7 HOH A 40 226 40 HOH HOH . Z 7 HOH A 41 227 41 HOH HOH . Z 7 HOH A 42 228 42 HOH HOH . Z 7 HOH A 43 229 43 HOH HOH . Z 7 HOH A 44 230 44 HOH HOH . Z 7 HOH A 45 231 45 HOH HOH . Z 7 HOH A 46 232 46 HOH HOH . Z 7 HOH A 47 233 47 HOH HOH . Z 7 HOH A 48 234 48 HOH HOH . Z 7 HOH A 49 235 49 HOH HOH . Z 7 HOH A 50 236 50 HOH HOH . Z 7 HOH A 51 237 51 HOH HOH . Z 7 HOH A 52 238 52 HOH HOH . Z 7 HOH A 53 239 53 HOH HOH . Z 7 HOH A 54 240 54 HOH HOH . Z 7 HOH A 55 241 55 HOH HOH . Z 7 HOH A 56 242 56 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 C C1 MPD . . . M 3 8.084 44.639 16.749 0.5 30.5 ? C1 MPD 174 A 1 HETATM 2 C C2 MPD . . . M 3 8.509 45.23 18.088 0.5 32.09 ? C2 MPD 174 A 1 HETATM 3 O O2 MPD . . . M 3 7.949 44.414 19.127 0.5 35.39 ? O2 MPD 174 A 1 HETATM 4 C CM MPD . . . M 3 10.039 45.13 18.158 0.5 33.25 ? CM MPD 174 A 1 HETATM 5 C C3 MPD . . . M 3 8.097 46.664 18.403 0.5 30.57 ? C3 MPD 174 A 1 HETATM 6 C C4 MPD . . . M 3 6.608 46.875 18.615 0.5 29.49 ? C4 MPD 174 A 1 HETATM 7 O O4 MPD . . . M 3 6.102 45.889 19.498 0.5 30.32 ? O4 MPD 174 A 1 HETATM 8 C C5 MPD . . . M 3 6.33 48.289 19.079 0.5 28.17 ? C5 MPD 174 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #