data_6DZ1 # _model_server_result.job_id JuRWLYGMRw7pdlIFlcVw_A _model_server_result.datetime_utc '2024-10-19 15:30:33' _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 6dz1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":205}' # _entry.id 6DZ1 # _exptl.entry_id 6DZ1 _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 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 6DZ1 _cell.length_a 68.07 _cell.length_b 68.07 _cell.length_c 89.38 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DZ1 _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,P 1 1,2,4,6 B,I,J,K,L,M,N,O,Q 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 68.07 68.07 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 68.07 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 68.07 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 G N N ? 3 H N N ? 3 M 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 44 A THR 63 1_555 E K K . A K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc2 A O THR 44 A THR 63 1_555 E K K . A K 203 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc3 A O THR 44 A THR 63 1_555 F K K . A K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc4 A OG1 THR 44 A THR 63 1_555 F K K . A K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc5 A O THR 44 A THR 63 1_555 F K K . A K 204 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? metalc ? metalc6 A OG1 THR 44 A THR 63 1_555 F K K . A K 204 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc7 A O VAL 45 A VAL 64 1_555 D K K . A K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc8 A O VAL 45 A VAL 64 1_555 D K K . A K 202 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc9 A O VAL 45 A VAL 64 1_555 E K K . A K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc10 A O VAL 45 A VAL 64 1_555 E K K . A K 203 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc11 A O GLY 46 A GLY 65 1_555 C K K . A K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.223 ? metalc ? metalc12 A O GLY 46 A GLY 65 1_555 C K K . A K 201 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 3.223 ? metalc ? metalc13 A O GLY 46 A GLY 65 1_555 D K K . A K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc14 A O GLY 46 A GLY 65 1_555 D K K . A K 202 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc15 A O TYR 47 A TYR 66 1_555 C K K . A K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc16 A O TYR 47 A TYR 66 1_555 C K K . A K 201 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc17 B O SER 24 B SER 43 1_555 N K K . B K 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc18 B O LEU 29 B LEU 48 1_555 N K K . B K 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc19 B O THR 44 B THR 63 1_555 K K K . B K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc20 B O THR 44 B THR 63 1_555 K K K . B K 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc21 B O THR 44 B THR 63 1_555 L K K . B K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.111 ? metalc ? metalc22 B OG1 THR 44 B THR 63 1_555 L K K . B K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? metalc ? metalc23 B O THR 44 B THR 63 1_555 L K K . B K 204 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc24 B OG1 THR 44 B THR 63 1_555 L K K . B K 204 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc25 B O VAL 45 B VAL 64 1_555 J K K . B K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc26 B O VAL 45 B VAL 64 1_555 J K K . B K 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc27 B O VAL 45 B VAL 64 1_555 K K K . B K 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc28 B O VAL 45 B VAL 64 1_555 K K K . B K 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc29 B O GLY 46 B GLY 65 1_555 I K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.125 ? metalc ? metalc30 B O GLY 46 B GLY 65 1_555 I K K . B K 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.125 ? metalc ? metalc31 B O GLY 46 B GLY 65 1_555 J K K . B K 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc32 B O GLY 46 B GLY 65 1_555 J K K . B K 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc33 B O TYR 47 B TYR 66 1_555 I K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc34 B O TYR 47 B TYR 66 1_555 I K K . B K 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? # _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 205 n n C1 H11 MPD sing 206 n n C1 H12 MPD sing 207 n n C1 H13 MPD sing 208 n n C2 O2 MPD sing 209 n n C2 CM MPD sing 210 n n C2 C3 MPD sing 211 n n O2 HO2 MPD sing 212 n n CM HM1 MPD sing 213 n n CM HM2 MPD sing 214 n n CM HM3 MPD sing 215 n n C3 C4 MPD sing 216 n n C3 H31 MPD sing 217 n n C3 H32 MPD sing 218 n n C4 O4 MPD sing 219 n n C4 C5 MPD sing 220 n n C4 H4 MPD sing 221 n n O4 HO4 MPD sing 222 n n C5 H51 MPD sing 223 n n C5 H52 MPD sing 224 n n C5 H53 MPD sing 225 n n # _atom_sites.entry_id 6DZ1 _atom_sites.fract_transf_matrix[1][1] 0.014691 _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] 0.014691 _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] 0.011188 _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 2 K A 1 204 4 K K . G 3 MPD A 1 205 1 MPD MPD . H 3 MPD A 1 206 2 MPD MPD . I 2 K B 1 201 1 K K . J 2 K B 1 202 2 K K . K 2 K B 1 203 3 K K . L 2 K B 1 204 4 K K . M 3 MPD B 1 205 3 MPD MPD . N 2 K B 1 206 1 K K . O 2 K B 1 207 2 K K . P 4 HOH A 1 301 78 HOH HOH . P 4 HOH A 2 302 76 HOH HOH . P 4 HOH A 3 303 17 HOH WAT . P 4 HOH A 4 304 5 HOH WAT . P 4 HOH A 5 305 75 HOH HOH . P 4 HOH A 6 306 9 HOH WAT . P 4 HOH A 7 307 50 HOH WAT . P 4 HOH A 8 308 34 HOH WAT . P 4 HOH A 9 309 71 HOH WAT . P 4 HOH A 10 310 84 HOH HOH . P 4 HOH A 11 311 79 HOH HOH . P 4 HOH A 12 312 81 HOH HOH . Q 4 HOH B 1 301 41 HOH WAT . Q 4 HOH B 2 302 8 HOH WAT . Q 4 HOH B 3 303 16 HOH WAT . Q 4 HOH B 4 304 6 HOH WAT . Q 4 HOH B 5 305 7 HOH WAT . Q 4 HOH B 6 306 15 HOH WAT . Q 4 HOH B 7 307 25 HOH WAT . Q 4 HOH B 8 308 49 HOH WAT . Q 4 HOH B 9 309 33 HOH WAT . Q 4 HOH B 10 310 39 HOH WAT . Q 4 HOH B 11 311 80 HOH HOH . Q 4 HOH B 12 312 55 HOH WAT . Q 4 HOH B 13 313 82 HOH HOH . Q 4 HOH B 14 314 60 HOH WAT . # 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 3 14.108 36.176 11.656 1 46.18 ? C1 MPD 205 A 1 HETATM 2 C C2 MPD . . . G 3 15.519 35.659 11.882 1 55.57 ? C2 MPD 205 A 1 HETATM 3 O O2 MPD . . . G 3 15.924 36.017 13.227 1 64.32 ? O2 MPD 205 A 1 HETATM 4 C CM MPD . . . G 3 15.501 34.138 11.794 1 52.13 ? CM MPD 205 A 1 HETATM 5 C C3 MPD . . . G 3 16.514 36.23 10.863 1 46.77 ? C3 MPD 205 A 1 HETATM 6 C C4 MPD . . . G 3 16.347 37.728 10.599 1 48.51 ? C4 MPD 205 A 1 HETATM 7 O O4 MPD . . . G 3 17.432 38.434 11.166 1 52.69 ? O4 MPD 205 A 1 HETATM 8 C C5 MPD . . . G 3 16.324 38.02 9.101 1 52.14 ? C5 MPD 205 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 8 #