data_8CU1 # _model_server_result.job_id Wgxwl8ax-HR61TKWnkVWgQ _model_server_result.datetime_utc '2024-10-10 01:22:49' _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 8cu1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":205}' # _entry.id 8CU1 # _exptl.entry_id 8CU1 _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 17 _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 8CU1 _cell.length_a 68.816 _cell.length_b 68.816 _cell.length_c 90.365 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CU1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall 'I 4' _symmetry.space_group_name_H-M 'I 4' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,I,J,K,L,M,N,O,P,HA 1 1 A,D,E,F,G,H,I,J,K,L,M,N,O,P,HA 1 2 A,D,E,F,G,H,I,J,K,L,M,N,O,P,HA 1 3 A,D,E,F,G,H,I,J,K,L,M,N,O,P,HA 1 4 B,C,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 2 1 B,C,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 2 2 B,C,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 2 3 B,C,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,IA 2 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 V N N ? 3 W N N ? 3 X N N ? 3 Y N N ? 3 Z N N ? 3 AA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 GLC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GLC 1 D 1 GLC E 1 MAL 2 n C GLC 2 D 2 GLC E 1 MAL # 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 C O4 GLC . D GLC 1 1_555 C C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc1 A O THR 45 A THR 63 1_555 L K K . A K 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc2 A O THR 45 A THR 63 1_555 L K K . A K 209 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc3 A O THR 45 A THR 63 1_555 M K K . A K 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc4 A OG1 THR 45 A THR 63 1_555 M K K . A K 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc5 A O THR 45 A THR 63 1_555 M K K . A K 210 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc6 A OG1 THR 45 A THR 63 1_555 M K K . A K 210 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc7 A O VAL 46 A VAL 64 1_555 K K K . A K 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc8 A O VAL 46 A VAL 64 1_555 K K K . A K 208 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc9 A O VAL 46 A VAL 64 1_555 L K K . A K 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc10 A O VAL 46 A VAL 64 1_555 L K K . A K 209 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc11 A O GLY 47 A GLY 65 1_555 J K K . A K 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.27 ? metalc ? metalc12 A O GLY 47 A GLY 65 1_555 J K K . A K 207 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.27 ? metalc ? metalc13 A O GLY 47 A GLY 65 1_555 K K K . A K 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc14 A O GLY 47 A GLY 65 1_555 K K K . A K 208 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc15 A O TYR 48 A TYR 66 1_555 J K K . A K 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc16 A O TYR 48 A TYR 66 1_555 J K K . A K 207 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc17 O K K . A K 212 1_555 HA O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.244 ? metalc ? metalc18 O K K . A K 212 1_555 HA O HOH . A HOH 323 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.244 ? metalc ? metalc19 B O THR 45 B THR 63 1_555 DA K K . B K 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc20 B O THR 45 B THR 63 1_555 DA K K . B K 214 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc21 B O THR 45 B THR 63 1_555 EA K K . B K 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc22 B OG1 THR 45 B THR 63 1_555 EA K K . B K 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc23 B O THR 45 B THR 63 1_555 EA K K . B K 215 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc24 B OG1 THR 45 B THR 63 1_555 EA K K . B K 215 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc25 B O VAL 46 B VAL 64 1_555 CA K K . B K 213 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc26 B O VAL 46 B VAL 64 1_555 CA K K . B K 213 2_555 ? A ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc27 B O VAL 46 B VAL 64 1_555 DA K K . B K 214 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc28 B O VAL 46 B VAL 64 1_555 DA K K . B K 214 2_555 ? A ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc29 B O GLY 47 B GLY 65 1_555 BA K K . B K 212 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.023 ? metalc ? metalc30 B O GLY 47 B GLY 65 1_555 BA K K . B K 212 2_555 ? A ? ? ? ? ? ? ? ? ? ? 3.023 ? metalc ? metalc31 B O GLY 47 B GLY 65 1_555 CA K K . B K 213 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc32 B O GLY 47 B GLY 65 1_555 CA K K . B K 213 2_555 ? A ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc33 B O TYR 48 B TYR 66 1_555 BA K K . B K 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc34 B O TYR 48 B TYR 66 1_555 BA K K . B K 212 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc35 B O GLY 49 B GLY 67 1_555 GA K K . B K 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? # _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 229 n n C1 H11 MPD sing 230 n n C1 H12 MPD sing 231 n n C1 H13 MPD sing 232 n n C2 O2 MPD sing 233 n n C2 CM MPD sing 234 n n C2 C3 MPD sing 235 n n O2 HO2 MPD sing 236 n n CM HM1 MPD sing 237 n n CM HM2 MPD sing 238 n n CM HM3 MPD sing 239 n n C3 C4 MPD sing 240 n n C3 H31 MPD sing 241 n n C3 H32 MPD sing 242 n n C4 O4 MPD sing 243 n n C4 C5 MPD sing 244 n n C4 H4 MPD sing 245 n n O4 HO4 MPD sing 246 n n C5 H51 MPD sing 247 n n C5 H52 MPD sing 248 n n C5 H53 MPD sing 249 n n # _atom_sites.entry_id 8CU1 _atom_sites.fract_transf_matrix[1][1] 0.014532 _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] 0.014532 _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] 0.011066 _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 D 3 MPD A 1 201 1 MPD MPD . E 3 MPD A 1 202 3 MPD MPD . F 3 MPD A 1 203 8 MPD MPD . G 3 MPD A 1 204 11 MPD MPD . H 3 MPD A 1 205 12 MPD MPD . I 3 MPD A 1 206 14 MPD MPD . J 4 K A 1 207 1 K K . K 4 K A 1 208 2 K K . L 4 K A 1 209 3 K K . M 4 K A 1 210 4 K K . N 4 K A 1 211 5 K K . O 4 K A 1 212 14 K K . P 4 K A 1 213 15 K K . Q 3 MPD B 1 201 5 MPD MPD . R 3 MPD B 1 202 6 MPD MPD . S 3 MPD B 1 203 7 MPD MPD . T 3 MPD B 1 204 9 MPD MPD . U 3 MPD B 1 205 10 MPD MPD . V 3 MPD B 1 206 13 MPD MPD . W 3 MPD B 1 207 16 MPD MPD . X 3 MPD B 1 208 17 MPD MPD . Y 3 MPD B 1 209 20 MPD MPD . Z 3 MPD B 1 210 21 MPD MPD . AA 3 MPD B 1 211 22 MPD MPD . BA 4 K B 1 212 7 K K . CA 4 K B 1 213 8 K K . DA 4 K B 1 214 9 K K . EA 4 K B 1 215 10 K K . FA 4 K B 1 216 11 K K . GA 4 K B 1 217 12 K K . HA 5 HOH A 1 301 12 HOH HOH . HA 5 HOH A 2 302 3 HOH HOH . HA 5 HOH A 3 303 8 HOH HOH . HA 5 HOH A 4 304 13 HOH HOH . HA 5 HOH A 5 305 21 HOH HOH . HA 5 HOH A 6 306 53 HOH HOH . HA 5 HOH A 7 307 15 HOH HOH . HA 5 HOH A 8 308 9 HOH HOH . HA 5 HOH A 9 309 14 HOH HOH . HA 5 HOH A 10 310 20 HOH HOH . HA 5 HOH A 11 311 63 HOH HOH . HA 5 HOH A 12 312 10 HOH HOH . HA 5 HOH A 13 313 26 HOH HOH . HA 5 HOH A 14 314 62 HOH HOH . HA 5 HOH A 15 315 38 HOH HOH . HA 5 HOH A 16 316 55 HOH HOH . HA 5 HOH A 17 317 49 HOH HOH . HA 5 HOH A 18 318 27 HOH HOH . HA 5 HOH A 19 319 57 HOH HOH . HA 5 HOH A 20 320 25 HOH HOH . HA 5 HOH A 21 321 61 HOH HOH . HA 5 HOH A 22 322 44 HOH HOH . HA 5 HOH A 23 323 40 HOH HOH . IA 5 HOH B 1 301 5 HOH HOH . IA 5 HOH B 2 302 66 HOH HOH . IA 5 HOH B 3 303 24 HOH HOH . IA 5 HOH B 4 304 64 HOH HOH . IA 5 HOH B 5 305 1 HOH HOH . IA 5 HOH B 6 306 17 HOH HOH . IA 5 HOH B 7 307 7 HOH HOH . IA 5 HOH B 8 308 2 HOH HOH . IA 5 HOH B 9 309 4 HOH HOH . IA 5 HOH B 10 310 54 HOH HOH . IA 5 HOH B 11 311 6 HOH HOH . IA 5 HOH B 12 312 22 HOH HOH . IA 5 HOH B 13 313 67 HOH HOH . IA 5 HOH B 14 314 11 HOH HOH . IA 5 HOH B 15 315 60 HOH HOH . IA 5 HOH B 16 316 16 HOH HOH . IA 5 HOH B 17 317 50 HOH HOH . IA 5 HOH B 18 318 65 HOH HOH . IA 5 HOH B 19 319 68 HOH HOH . IA 5 HOH B 20 320 48 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 . . . U 3 -13.946 -12.149 -39.003 1 54.1 ? C1 MPD 205 B 1 HETATM 2 C C2 MPD . . . U 3 -13.299 -11.508 -37.781 1 48.17 ? C2 MPD 205 B 1 HETATM 3 O O2 MPD . . . U 3 -14.095 -10.372 -37.362 1 53.19 ? O2 MPD 205 B 1 HETATM 4 C CM MPD . . . U 3 -13.269 -12.51 -36.635 1 45.85 ? CM MPD 205 B 1 HETATM 5 C C3 MPD . . . U 3 -11.885 -11.041 -38.118 1 55.31 ? C3 MPD 205 B 1 HETATM 6 C C4 MPD . . . U 3 -11.919 -9.855 -39.073 1 60.58 ? C4 MPD 205 B 1 HETATM 7 O O4 MPD . . . U 3 -11.893 -8.642 -38.352 1 87.89 ? O4 MPD 205 B 1 HETATM 8 C C5 MPD . . . U 3 -10.742 -9.879 -40.043 1 52.75 ? C5 MPD 205 B 1 HETATM 9 H H11 MPD . . . U 3 -13.275 -12.066 -39.857 1 64.92 ? H11 MPD 205 B 1 HETATM 10 H H12 MPD . . . U 3 -14.881 -11.635 -39.227 1 64.92 ? H12 MPD 205 B 1 HETATM 11 H H13 MPD . . . U 3 -14.15 -13.203 -38.821 1 64.92 ? H13 MPD 205 B 1 HETATM 12 H HO2 MPD . . . U 3 -13.516 -9.598 -37.203 1 63.83 ? HO2 MPD 205 B 1 HETATM 13 H HM1 MPD . . . U 3 -12.29 -12.988 -36.598 1 55.02 ? HM1 MPD 205 B 1 HETATM 14 H HM2 MPD . . . U 3 -14.045 -13.265 -36.758 1 55.02 ? HM2 MPD 205 B 1 HETATM 15 H HM3 MPD . . . U 3 -13.438 -11.979 -35.698 1 55.02 ? HM3 MPD 205 B 1 HETATM 16 H H31 MPD . . . U 3 -11.36 -10.771 -37.202 1 66.38 ? H31 MPD 205 B 1 HETATM 17 H H32 MPD . . . U 3 -11.346 -11.867 -38.579 1 66.38 ? H32 MPD 205 B 1 HETATM 18 H H4 MPD . . . U 3 -12.829 -9.904 -39.665 1 72.7 ? H4 MPD 205 B 1 HETATM 19 H HO4 MPD . . . U 3 -11.706 -8.817 -37.406 1 105.47 ? HO4 MPD 205 B 1 HETATM 20 H H51 MPD . . . U 3 -10.268 -8.897 -40.059 1 63.3 ? H51 MPD 205 B 1 HETATM 21 H H52 MPD . . . U 3 -11.1 -10.126 -41.043 1 63.3 ? H52 MPD 205 B 1 HETATM 22 H H53 MPD . . . U 3 -10.012 -10.623 -39.725 1 63.3 ? H53 MPD 205 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #