data_8A7X # _model_server_result.job_id Xy9tS_g40zkxTTHB1AWI4w _model_server_result.datetime_utc '2025-09-07 11:06:21' _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 8a7x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":208}' # _entry.id 8A7X # _exptl.entry_id 8A7X _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 18 _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 8A7X _cell.length_a 68.16 _cell.length_b 68.16 _cell.length_c 90.25 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8A7X _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,C,D,E,F,G,H,I,J,K,L,M,N,DA 1 1,2,4,6 B,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,EA 2 1,3,5,7 # 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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 68.16 68.16 0 3 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 4 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 68.16 0 0 5 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 6 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 68.16 0 7 '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 J 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 ? 3 BA 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 THR 46 A THR 63 1_555 C CS CS . A CS 201 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.804 ? metalc ? metalc2 A O THR 46 A THR 63 1_555 C CS CS . A CS 201 3_655 ? ? ? ? A ? ? ? ? ? ? ? 2.812 ? metalc ? metalc3 A O THR 46 A THR 63 1_555 L K K . A K 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? metalc ? metalc4 A OG1 THR 46 A THR 63 1_555 L K K . A K 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc5 A O THR 46 A THR 63 1_555 L K K . A K 210 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? metalc ? metalc6 A OG1 THR 46 A THR 63 1_555 L K K . A K 210 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc7 A OG1 THR 46 A THR 63 1_555 M K K . A K 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.411 ? metalc ? metalc8 A OG1 THR 46 A THR 63 1_555 M K K . A K 211 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.411 ? metalc ? metalc9 A O VAL 47 A VAL 64 1_555 C CS CS . A CS 201 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.172 ? metalc ? metalc10 A O VAL 47 A VAL 64 1_555 C CS CS . A CS 201 1_555 ? ? ? ? B ? ? ? ? ? ? ? 3.089 ? metalc ? metalc11 A O VAL 47 A VAL 64 1_555 C CS CS . A CS 201 3_655 ? ? ? ? A ? ? ? ? ? ? ? 2.853 ? metalc ? metalc12 A O VAL 47 A VAL 64 1_555 C CS CS . A CS 201 3_655 ? ? ? ? B ? ? ? ? ? ? ? 3.089 ? metalc ? metalc13 A O SER 52 A SER 69 1_555 N K K . A K 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.262 ? metalc ? metalc14 A O PRO 53 A PRO 70 1_555 N K K . A K 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.486 ? metalc ? metalc15 D O2 MPD . A MPD 202 1_555 N K K . A K 212 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.423 ? metalc ? metalc16 K K K . A K 209 1_555 DA O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc17 K K K . A K 209 1_555 DA O HOH . A HOH 308 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc18 B O THR 46 B THR 63 1_555 O CS CS . B CS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.121 ? metalc ? metalc19 B O THR 46 B THR 63 1_555 O CS CS . B CS 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.121 ? metalc ? metalc20 B O THR 46 B THR 63 1_555 P CS CS . B CS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc21 B OG1 THR 46 B THR 63 1_555 P CS CS . B CS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc22 B O THR 46 B THR 63 1_555 P CS CS . B CS 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc23 B OG1 THR 46 B THR 63 1_555 P CS CS . B CS 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc24 B OG1 THR 46 B THR 63 1_555 CA K K . B K 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.495 ? metalc ? metalc25 B OG1 THR 46 B THR 63 1_555 CA K K . B K 215 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.495 ? metalc ? metalc26 B O VAL 47 B VAL 64 1_555 O CS CS . B CS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc27 B O VAL 47 B VAL 64 1_555 O CS CS . B CS 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? # _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 237 n n C1 H11 MPD sing 238 n n C1 H12 MPD sing 239 n n C1 H13 MPD sing 240 n n C2 O2 MPD sing 241 n n C2 CM MPD sing 242 n n C2 C3 MPD sing 243 n n O2 HO2 MPD sing 244 n n CM HM1 MPD sing 245 n n CM HM2 MPD sing 246 n n CM HM3 MPD sing 247 n n C3 C4 MPD sing 248 n n C3 H31 MPD sing 249 n n C3 H32 MPD sing 250 n n C4 O4 MPD sing 251 n n C4 C5 MPD sing 252 n n C4 H4 MPD sing 253 n n O4 HO4 MPD sing 254 n n C5 H51 MPD sing 255 n n C5 H52 MPD sing 256 n n C5 H53 MPD sing 257 n n # _atom_sites.entry_id 8A7X _atom_sites.fract_transf_matrix[1][1] 0.014671 _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] 0.014671 _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] 0.01108 _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 C 2 CS A 1 201 1 CS CS . D 3 MPD A 1 202 1 MPD MPD . E 3 MPD A 1 203 4 MPD MPD . F 3 MPD A 1 204 5 MPD MPD . G 3 MPD A 1 205 6 MPD MPD . H 3 MPD A 1 206 10 MPD MPD . I 3 MPD A 1 207 13 MPD MPD . J 3 MPD A 1 208 15 MPD MPD . K 4 K A 1 209 1 K K . L 4 K A 1 210 2 K K . M 4 K A 1 211 3 K K . N 4 K A 1 212 5 K K . O 2 CS B 1 201 2 CS CS . P 2 CS B 1 202 3 CS CS . Q 2 CS B 1 203 4 CS CS . R 3 MPD B 1 204 2 MPD MPD . S 3 MPD B 1 205 3 MPD MPD . T 3 MPD B 1 206 7 MPD MPD . U 3 MPD B 1 207 8 MPD MPD . V 3 MPD B 1 208 9 MPD MPD . W 3 MPD B 1 209 11 MPD MPD . X 3 MPD B 1 210 12 MPD MPD . Y 3 MPD B 1 211 14 MPD MPD . Z 3 MPD B 1 212 16 MPD MPD . AA 3 MPD B 1 213 17 MPD MPD . BA 3 MPD B 1 214 18 MPD MPD . CA 4 K B 1 215 4 K K . DA 5 HOH A 1 301 17 HOH HOH . DA 5 HOH A 2 302 2 HOH HOH . DA 5 HOH A 3 303 18 HOH HOH . DA 5 HOH A 4 304 3 HOH HOH . DA 5 HOH A 5 305 6 HOH HOH . DA 5 HOH A 6 306 15 HOH HOH . DA 5 HOH A 7 307 5 HOH HOH . DA 5 HOH A 8 308 8 HOH HOH . DA 5 HOH A 9 309 14 HOH HOH . DA 5 HOH A 10 310 27 HOH HOH . DA 5 HOH A 11 311 19 HOH HOH . DA 5 HOH A 12 312 22 HOH HOH . DA 5 HOH A 13 313 23 HOH HOH . DA 5 HOH A 14 314 10 HOH HOH . DA 5 HOH A 15 315 28 HOH HOH . EA 5 HOH B 1 301 12 HOH HOH . EA 5 HOH B 2 302 7 HOH HOH . EA 5 HOH B 3 303 9 HOH HOH . EA 5 HOH B 4 304 4 HOH HOH . EA 5 HOH B 5 305 1 HOH HOH . EA 5 HOH B 6 306 20 HOH HOH . EA 5 HOH B 7 307 21 HOH HOH . EA 5 HOH B 8 308 13 HOH HOH . EA 5 HOH B 9 309 16 HOH HOH . EA 5 HOH B 10 310 25 HOH HOH . EA 5 HOH B 11 311 11 HOH HOH . EA 5 HOH B 12 312 26 HOH HOH . EA 5 HOH B 13 313 24 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 . . . V 3 3.217 27.361 53.3 1 116.29 ? C1 MPD 208 B 1 HETATM 2 C C2 MPD . . . V 3 2.239 26.582 52.358 1 115.54 ? C2 MPD 208 B 1 HETATM 3 O O2 MPD . . . V 3 1.373 25.853 53.186 1 114.24 ? O2 MPD 208 B 1 HETATM 4 C CM MPD . . . V 3 1.441 27.567 51.588 1 102.02 ? CM MPD 208 B 1 HETATM 5 C C3 MPD . . . V 3 2.982 25.667 51.334 1 111.53 ? C3 MPD 208 B 1 HETATM 6 C C4 MPD . . . V 3 3.271 24.268 51.918 1 108.36 ? C4 MPD 208 B 1 HETATM 7 O O4 MPD . . . V 3 3.886 23.428 50.979 1 92.11 ? O4 MPD 208 B 1 HETATM 8 C C5 MPD . . . V 3 4.096 24.37 53.163 1 105.09 ? C5 MPD 208 B 1 HETATM 9 H H11 MPD . . . V 3 3.43 26.861 54.104 1 139.65 ? H11 MPD 208 B 1 HETATM 10 H H12 MPD . . . V 3 4.062 27.561 52.868 1 139.65 ? H12 MPD 208 B 1 HETATM 11 H H13 MPD . . . V 3 2.848 28.21 53.592 1 139.65 ? H13 MPD 208 B 1 HETATM 12 H HO2 MPD . . . V 3 0.943 26.407 53.672 1 137.19 ? HO2 MPD 208 B 1 HETATM 13 H HM1 MPD . . . V 3 2.028 28.136 51.065 1 122.52 ? HM1 MPD 208 B 1 HETATM 14 H HM2 MPD . . . V 3 0.833 27.109 50.987 1 122.52 ? HM2 MPD 208 B 1 HETATM 15 H HM3 MPD . . . V 3 0.925 28.123 52.192 1 122.52 ? HM3 MPD 208 B 1 HETATM 16 H H31 MPD . . . V 3 2.462 25.584 50.518 1 133.93 ? H31 MPD 208 B 1 HETATM 17 H H32 MPD . . . V 3 3.81 26.084 51.049 1 133.93 ? H32 MPD 208 B 1 HETATM 18 H H4 MPD . . . V 3 2.432 23.831 52.132 1 130.14 ? H4 MPD 208 B 1 HETATM 19 H HO4 MPD . . . V 3 4.724 23.574 50.995 1 110.63 ? HO4 MPD 208 B 1 HETATM 20 H H51 MPD . . . V 3 4.517 23.52 53.365 1 126.2 ? H51 MPD 208 B 1 HETATM 21 H H52 MPD . . . V 3 4.792 25.037 53.059 1 126.2 ? H52 MPD 208 B 1 HETATM 22 H H53 MPD . . . V 3 3.543 24.622 53.92 1 126.2 ? H53 MPD 208 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #