data_4PDL # _model_server_result.job_id 6SK1-4F-PkZLub1Cg7gQ3w _model_server_result.datetime_utc '2024-10-19 21:28:43' _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 4pdl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":205}' # _entry.id 4PDL # _exptl.entry_id 4PDL _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 3 _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 4PDL _cell.length_a 68.106 _cell.length_b 68.106 _cell.length_c 89.593 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PDL _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,N 1 1,2,3,4 B,J,K,L,M,O 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 G N N ? 4 H N N ? 4 L 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 CS CS . A CS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.194 ? metalc ? metalc2 A O THR 46 A THR 63 1_555 D CS CS . A CS 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.194 ? metalc ? metalc3 A O THR 46 A THR 63 1_555 F NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc4 A OG1 THR 46 A THR 63 1_555 F NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc5 A O THR 46 A THR 63 1_555 F NA NA . A NA 204 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc6 A OG1 THR 46 A THR 63 1_555 F NA NA . A NA 204 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc7 A O VAL 47 A VAL 64 1_555 D CS CS . A CS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc8 A O VAL 47 A VAL 64 1_555 D CS CS . A CS 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc9 A O GLY 48 A GLY 65 1_555 E CS CS . A CS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc10 A O GLY 48 A GLY 65 1_555 E CS CS . A CS 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc11 A O TYR 49 A TYR 66 1_555 C CS CS . A CS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc12 A O TYR 49 A TYR 66 1_555 E CS CS . A CS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.021 ? metalc ? metalc13 A O TYR 49 A TYR 66 1_555 E CS CS . A CS 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.021 ? metalc ? metalc14 A O GLY 50 A GLY 67 1_555 C CS CS . A CS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.48 ? metalc ? metalc15 C CS CS . A CS 201 1_555 N O HOH . A HOH 306 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.19 ? metalc ? metalc16 B O THR 46 B THR 63 1_555 J CS CS . B CS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.215 ? metalc ? metalc17 B O THR 46 B THR 63 1_555 J CS CS . B CS 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.215 ? metalc ? metalc18 B O VAL 47 B VAL 64 1_555 J CS CS . B CS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc19 B O VAL 47 B VAL 64 1_555 J CS CS . B CS 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc20 B O GLY 48 B GLY 65 1_555 K CS CS . B CS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? metalc ? metalc21 B O GLY 48 B GLY 65 1_555 K CS CS . B CS 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? metalc ? metalc22 B O TYR 49 B TYR 66 1_555 K CS CS . B CS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.148 ? metalc ? metalc23 B O TYR 49 B TYR 66 1_555 K CS CS . B CS 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.148 ? # _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 243 n n C1 H11 MPD sing 244 n n C1 H12 MPD sing 245 n n C1 H13 MPD sing 246 n n C2 O2 MPD sing 247 n n C2 CM MPD sing 248 n n C2 C3 MPD sing 249 n n O2 HO2 MPD sing 250 n n CM HM1 MPD sing 251 n n CM HM2 MPD sing 252 n n CM HM3 MPD sing 253 n n C3 C4 MPD sing 254 n n C3 H31 MPD sing 255 n n C3 H32 MPD sing 256 n n C4 O4 MPD sing 257 n n C4 C5 MPD sing 258 n n C4 H4 MPD sing 259 n n O4 HO4 MPD sing 260 n n C5 H51 MPD sing 261 n n C5 H52 MPD sing 262 n n C5 H53 MPD sing 263 n n # _atom_sites.entry_id 4PDL _atom_sites.fract_transf_matrix[1][1] 0.014683 _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] 0.014683 _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] 0.011162 _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 2 CS A 1 202 2 CS CS . E 2 CS A 1 203 3 CS CS . F 3 NA A 1 204 6 NA NA . G 4 MPD A 1 205 1 MPD MPD . H 4 MPD A 1 206 3 MPD MPD . I 5 HEX A 1 207 2 HEX HEX . J 2 CS B 1 201 4 CS CS . K 2 CS B 1 202 5 CS CS . L 4 MPD B 1 203 2 MPD MPD . M 5 HEX B 1 204 1 HEX HEX . N 6 HOH A 1 301 54 HOH HOH . N 6 HOH A 2 302 10 HOH HOH . N 6 HOH A 3 303 15 HOH HOH . N 6 HOH A 4 304 14 HOH HOH . N 6 HOH A 5 305 8 HOH HOH . N 6 HOH A 6 306 25 HOH HOH . N 6 HOH A 7 307 2 HOH HOH . N 6 HOH A 8 308 39 HOH HOH . N 6 HOH A 9 309 21 HOH HOH . N 6 HOH A 10 310 11 HOH HOH . N 6 HOH A 11 311 4 HOH HOH . N 6 HOH A 12 312 31 HOH HOH . N 6 HOH A 13 313 50 HOH HOH . N 6 HOH A 14 314 1 HOH HOH . N 6 HOH A 15 315 3 HOH HOH . N 6 HOH A 16 316 7 HOH HOH . N 6 HOH A 17 317 9 HOH HOH . N 6 HOH A 18 318 12 HOH HOH . N 6 HOH A 19 319 19 HOH HOH . N 6 HOH A 20 320 23 HOH HOH . N 6 HOH A 21 321 34 HOH HOH . N 6 HOH A 22 322 35 HOH HOH . N 6 HOH A 23 323 40 HOH HOH . N 6 HOH A 24 324 45 HOH HOH . N 6 HOH A 25 325 46 HOH HOH . N 6 HOH A 26 326 47 HOH HOH . N 6 HOH A 27 327 48 HOH HOH . N 6 HOH A 28 328 49 HOH HOH . N 6 HOH A 29 329 53 HOH HOH . O 6 HOH B 1 301 13 HOH HOH . O 6 HOH B 2 302 6 HOH HOH . O 6 HOH B 3 303 20 HOH HOH . O 6 HOH B 4 304 26 HOH HOH . O 6 HOH B 5 305 24 HOH HOH . O 6 HOH B 6 306 33 HOH HOH . O 6 HOH B 7 307 42 HOH HOH . O 6 HOH B 8 308 38 HOH HOH . O 6 HOH B 9 309 16 HOH HOH . O 6 HOH B 10 310 22 HOH HOH . O 6 HOH B 11 311 17 HOH HOH . O 6 HOH B 12 312 27 HOH HOH . O 6 HOH B 13 313 30 HOH HOH . O 6 HOH B 14 314 32 HOH HOH . O 6 HOH B 15 315 37 HOH HOH . O 6 HOH B 16 316 41 HOH HOH . O 6 HOH B 17 317 43 HOH HOH . O 6 HOH B 18 318 44 HOH HOH . O 6 HOH B 19 319 55 HOH HOH . O 6 HOH B 20 320 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 . . . G 4 -13.968 -16.246 22.919 1 31.69 ? C1 MPD 205 A 1 HETATM 2 C C2 MPD . . . G 4 -14.503 -14.864 23.175 1 40.34 ? C2 MPD 205 A 1 HETATM 3 O O2 MPD . . . G 4 -14.906 -14.735 24.518 1 55.09 ? O2 MPD 205 A 1 HETATM 4 C CM MPD . . . G 4 -13.385 -13.889 22.937 1 35.63 ? CM MPD 205 A 1 HETATM 5 C C3 MPD . . . G 4 -15.724 -14.528 22.345 1 43.36 ? C3 MPD 205 A 1 HETATM 6 C C4 MPD . . . G 4 -16.997 -15.318 22.668 1 43.2 ? C4 MPD 205 A 1 HETATM 7 O O4 MPD . . . G 4 -18.01 -15.078 21.688 1 47.15 ? O4 MPD 205 A 1 HETATM 8 C C5 MPD . . . G 4 -16.753 -16.805 22.704 1 33.64 ? C5 MPD 205 A 1 HETATM 9 H H11 MPD . . . G 4 -14.473 -16.993 23.52 1 38.03 ? H11 MPD 205 A 1 HETATM 10 H H12 MPD . . . G 4 -12.912 -16.261 23.189 1 38.03 ? H12 MPD 205 A 1 HETATM 11 H H13 MPD . . . G 4 -14.052 -16.482 21.863 1 38.03 ? H13 MPD 205 A 1 HETATM 12 H HO2 MPD . . . G 4 -14.119 -14.758 25.101 1 66.1 ? HO2 MPD 205 A 1 HETATM 13 H HM1 MPD . . . G 4 -13.786 -12.965 22.522 1 42.76 ? HM1 MPD 205 A 1 HETATM 14 H HM2 MPD . . . G 4 -12.676 -14.314 22.228 1 42.76 ? HM2 MPD 205 A 1 HETATM 15 H HM3 MPD . . . G 4 -12.87 -13.677 23.872 1 42.76 ? HM3 MPD 205 A 1 HETATM 16 H H31 MPD . . . G 4 -15.48 -14.684 21.294 1 52.03 ? H31 MPD 205 A 1 HETATM 17 H H32 MPD . . . G 4 -15.944 -13.467 22.466 1 52.03 ? H32 MPD 205 A 1 HETATM 18 H H4 MPD . . . G 4 -17.358 -15.005 23.648 1 51.84 ? H4 MPD 205 A 1 HETATM 19 H HO4 MPD . . . G 4 -18.77 -14.623 22.108 1 56.58 ? HO4 MPD 205 A 1 HETATM 20 H H51 MPD . . . G 4 -16.564 -17.144 23.715 1 40.36 ? H51 MPD 205 A 1 HETATM 21 H H52 MPD . . . G 4 -17.68 -17.226 22.353 1 40.36 ? H52 MPD 205 A 1 HETATM 22 H H53 MPD . . . G 4 -15.995 -17.12 22.008 1 40.36 ? H53 MPD 205 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 22 #