data_4PDV # _model_server_result.job_id 3-rB9nmc0m3pYvSGC5yxzw _model_server_result.datetime_utc '2025-07-01 13:36:53' _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 4pdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":206}' # _entry.id 4PDV # _exptl.entry_id 4PDV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 4 _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 4PDV _cell.length_a 68.065 _cell.length_b 68.065 _cell.length_c 89.614 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PDV _symmetry.cell_setting . _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _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,P 1 1,2,3,4 B,J,K,L,M,N,O,Q 2 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_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 ? 4 H N N ? 4 I N N ? 4 N N N ? 4 O 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 D K K . A K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.36 ? metalc ? metalc2 A OG1 THR 46 A THR 63 1_555 D K K . A K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc3 A O THR 46 A THR 63 1_555 D K K . A K 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.36 ? metalc ? metalc4 A OG1 THR 46 A THR 63 1_555 D K K . A K 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc5 A O THR 46 A THR 63 1_555 G BA BA . A BA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc6 A O THR 46 A THR 63 1_555 G BA BA . A BA 205 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc7 A O VAL 47 A VAL 64 1_555 C K K . A K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc8 A O VAL 47 A VAL 64 1_555 C K K . A K 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc9 A O VAL 47 A VAL 64 1_555 G BA BA . A BA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc10 A O VAL 47 A VAL 64 1_555 G BA BA . A BA 205 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc11 A O GLY 48 A GLY 65 1_555 C K K . A K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc12 A O GLY 48 A GLY 65 1_555 C K K . A K 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc13 A O GLY 48 A GLY 65 1_555 E K K . A K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc14 A O GLY 48 A GLY 65 1_555 E K K . A K 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc15 A O TYR 49 A TYR 66 1_555 E K K . A K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc16 A O TYR 49 A TYR 66 1_555 E K K . A K 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc17 F BA BA . A BA 204 1_555 P O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc18 F BA BA . A BA 204 1_555 P O HOH . A HOH 311 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc19 F BA BA . A BA 204 1_555 P O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc20 F BA BA . A BA 204 1_555 P O HOH . A HOH 314 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc21 B O THR 46 B THR 63 1_555 J K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.069 ? metalc ? metalc22 B OG1 THR 46 B THR 63 1_555 J K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc23 B O THR 46 B THR 63 1_555 J K K . B K 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.069 ? metalc ? metalc24 B OG1 THR 46 B THR 63 1_555 J K K . B K 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc25 B O THR 46 B THR 63 1_555 M BA BA . B BA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc26 B O THR 46 B THR 63 1_555 M BA BA . B BA 204 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc27 B O VAL 47 B VAL 64 1_555 L K K . B K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc28 B O VAL 47 B VAL 64 1_555 L K K . B K 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc29 B O VAL 47 B VAL 64 1_555 M BA BA . B BA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc30 B O VAL 47 B VAL 64 1_555 M BA BA . B BA 204 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc31 B O GLY 48 B GLY 65 1_555 K K K . B K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc32 B O GLY 48 B GLY 65 1_555 K K K . B K 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc33 B O GLY 48 B GLY 65 1_555 L K K . B K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc34 B O GLY 48 B GLY 65 1_555 L K K . B K 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc35 B O TYR 49 B TYR 66 1_555 K K K . B K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc36 B O TYR 49 B TYR 66 1_555 K K K . B K 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? # _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 4PDV _atom_sites.fract_transf_matrix[1][1] 0.014692 _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] 0.014692 _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] 0.011159 _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 K A 1 201 1 K K . D 2 K A 1 202 2 K K . E 2 K A 1 203 3 K K . F 3 BA A 1 204 7 BA BA . G 3 BA A 1 205 8 BA BA . H 4 MPD A 1 206 1 MPD MPD . I 4 MPD A 1 207 2 MPD MPD . J 2 K B 1 201 4 K K . K 2 K B 1 202 5 K K . L 2 K B 1 203 6 K K . M 3 BA B 1 204 9 BA BA . N 4 MPD B 1 205 3 MPD MPD . O 4 MPD B 1 206 4 MPD MPD . P 5 HOH A 1 301 26 HOH HOH . P 5 HOH A 2 302 28 HOH HOH . P 5 HOH A 3 303 10 HOH HOH . P 5 HOH A 4 304 30 HOH HOH . P 5 HOH A 5 305 7 HOH HOH . P 5 HOH A 6 306 31 HOH HOH . P 5 HOH A 7 307 14 HOH HOH . P 5 HOH A 8 308 27 HOH HOH . P 5 HOH A 9 309 11 HOH HOH . P 5 HOH A 10 310 57 HOH HOH . P 5 HOH A 11 311 3 HOH HOH . P 5 HOH A 12 312 2 HOH HOH . P 5 HOH A 13 313 16 HOH HOH . P 5 HOH A 14 314 50 HOH HOH . P 5 HOH A 15 315 22 HOH HOH . P 5 HOH A 16 316 39 HOH HOH . P 5 HOH A 17 317 55 HOH HOH . P 5 HOH A 18 318 61 HOH HOH . P 5 HOH A 19 319 1 HOH HOH . P 5 HOH A 20 320 5 HOH HOH . P 5 HOH A 21 321 6 HOH HOH . P 5 HOH A 22 322 8 HOH HOH . P 5 HOH A 23 323 13 HOH HOH . P 5 HOH A 24 324 15 HOH HOH . P 5 HOH A 25 325 17 HOH HOH . P 5 HOH A 26 326 20 HOH HOH . P 5 HOH A 27 327 24 HOH HOH . P 5 HOH A 28 328 25 HOH HOH . P 5 HOH A 29 329 38 HOH HOH . P 5 HOH A 30 330 43 HOH HOH . P 5 HOH A 31 331 44 HOH HOH . P 5 HOH A 32 332 48 HOH HOH . P 5 HOH A 33 333 58 HOH HOH . P 5 HOH A 34 334 60 HOH HOH . P 5 HOH A 35 335 62 HOH HOH . Q 5 HOH B 1 301 37 HOH HOH . Q 5 HOH B 2 302 46 HOH HOH . Q 5 HOH B 3 303 51 HOH HOH . Q 5 HOH B 4 304 41 HOH HOH . Q 5 HOH B 5 305 4 HOH HOH . Q 5 HOH B 6 306 40 HOH HOH . Q 5 HOH B 7 307 32 HOH HOH . Q 5 HOH B 8 308 36 HOH HOH . Q 5 HOH B 9 309 35 HOH HOH . Q 5 HOH B 10 310 66 HOH HOH . Q 5 HOH B 11 311 54 HOH HOH . Q 5 HOH B 12 312 63 HOH HOH . Q 5 HOH B 13 313 59 HOH HOH . Q 5 HOH B 14 314 56 HOH HOH . Q 5 HOH B 15 315 9 HOH HOH . Q 5 HOH B 16 316 12 HOH HOH . Q 5 HOH B 17 317 18 HOH HOH . Q 5 HOH B 18 318 19 HOH HOH . Q 5 HOH B 19 319 29 HOH HOH . Q 5 HOH B 20 320 33 HOH HOH . Q 5 HOH B 21 321 34 HOH HOH . Q 5 HOH B 22 322 45 HOH HOH . Q 5 HOH B 23 323 49 HOH HOH . Q 5 HOH B 24 324 53 HOH HOH . Q 5 HOH B 25 325 64 HOH HOH . Q 5 HOH B 26 326 65 HOH HOH . Q 5 HOH B 27 327 67 HOH HOH . Q 5 HOH B 28 328 68 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 . . . H 4 -13.285 -14.006 22.813 1 37.1 ? C1 MPD 206 A 1 HETATM 2 C C2 MPD . . . H 4 -14.432 -14.907 23.154 1 38.39 ? C2 MPD 206 A 1 HETATM 3 O O2 MPD . . . H 4 -14.009 -16.245 22.963 1 40.1 ? O2 MPD 206 A 1 HETATM 4 C CM MPD . . . H 4 -14.81 -14.656 24.59 1 47.96 ? CM MPD 206 A 1 HETATM 5 C C3 MPD . . . H 4 -15.659 -14.636 22.317 1 43.39 ? C3 MPD 206 A 1 HETATM 6 C C4 MPD . . . H 4 -16.895 -15.421 22.743 1 41.86 ? C4 MPD 206 A 1 HETATM 7 O O4 MPD . . . H 4 -17.949 -15.21 21.808 1 51.72 ? O4 MPD 206 A 1 HETATM 8 C C5 MPD . . . H 4 -16.622 -16.899 22.735 1 36.75 ? C5 MPD 206 A 1 HETATM 9 H H11 MPD . . . H 4 -13.56 -13.374 21.969 1 44.53 ? H11 MPD 206 A 1 HETATM 10 H H12 MPD . . . H 4 -13.041 -13.377 23.668 1 44.53 ? H12 MPD 206 A 1 HETATM 11 H H13 MPD . . . H 4 -12.417 -14.609 22.547 1 44.53 ? H13 MPD 206 A 1 HETATM 12 H HO2 MPD . . . H 4 -14.294 -16.559 22.08 1 48.13 ? HO2 MPD 206 A 1 HETATM 13 H HM1 MPD . . . H 4 -13.911 -14.755 25.194 1 57.56 ? HM1 MPD 206 A 1 HETATM 14 H HM2 MPD . . . H 4 -15.243 -13.661 24.686 1 57.56 ? HM2 MPD 206 A 1 HETATM 15 H HM3 MPD . . . H 4 -15.522 -15.405 24.932 1 57.56 ? HM3 MPD 206 A 1 HETATM 16 H H31 MPD . . . H 4 -15.434 -14.873 21.277 1 52.06 ? H31 MPD 206 A 1 HETATM 17 H H32 MPD . . . H 4 -15.887 -13.571 22.364 1 52.06 ? H32 MPD 206 A 1 HETATM 18 H H4 MPD . . . H 4 -17.227 -15.109 23.732 1 50.23 ? H4 MPD 206 A 1 HETATM 19 H HO4 MPD . . . H 4 -18.719 -14.815 22.268 1 62.07 ? HO4 MPD 206 A 1 HETATM 20 H H51 MPD . . . H 4 -16.334 -17.232 21.747 1 44.1 ? H51 MPD 206 A 1 HETATM 21 H H52 MPD . . . H 4 -17.555 -17.351 23.014 1 44.1 ? H52 MPD 206 A 1 HETATM 22 H H53 MPD . . . H 4 -15.9 -17.188 23.49 1 44.1 ? H53 MPD 206 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #