data_8ECA # _model_server_result.job_id 2Tg5efs42hDqG9GlLgEjJw _model_server_result.datetime_utc '2025-03-04 23:07:39' _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 8eca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":101}' # _entry.id 8ECA # _exptl.entry_id 8ECA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 2 _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 120 _cell.entry_id 8ECA _cell.length_a 43.537 _cell.length_b 43.537 _cell.length_c 93.329 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ECA _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -31.109667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 K 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 disulf ? disulf1 A SG CYS 10 A CYS 10 1_555 C SG CYS 14 C CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 14 A CYS 14 1_555 D SG CYS 10 D CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 10 B CYS 10 1_555 E SG CYS 14 E CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 14 B CYS 14 1_555 F SG CYS 10 F CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 10 C CYS 10 1_555 D SG CYS 14 D CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 E SG CYS 10 E CYS 10 1_555 F SG CYS 14 F CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A C ORN 1 A ORN 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale2 A NE ORN 1 A ORN 1 1_555 A C VAL 16 A VAL 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale3 A C GLU 8 A GLU 8 1_555 A NE ORN 9 A ORN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale4 A C ORN 9 A ORN 9 1_555 A N CYS 10 A CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale5 A C ILE 12 A ILE 12 1_555 A N SAR 13 A SAR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C SAR 13 A SAR 13 1_555 A N CYS 14 A CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 B C ORN 1 B ORN 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale8 B NE ORN 1 B ORN 1 1_555 B C VAL 16 B VAL 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale9 B C GLU 8 B GLU 8 1_555 B NE ORN 9 B ORN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale10 B C ORN 9 B ORN 9 1_555 B N CYS 10 B CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale11 B C ILE 12 B ILE 12 1_555 B N SAR 13 B SAR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale12 B C SAR 13 B SAR 13 1_555 B N CYS 14 B CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 C C ORN 1 C ORN 1 1_555 C N LYS 2 C LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale14 C NE ORN 1 C ORN 1 1_555 C C VAL 16 C VAL 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale15 C C GLU 8 C GLU 8 1_555 C NE ORN 9 C ORN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.371 ? covale ? covale16 C C ORN 9 C ORN 9 1_555 C N CYS 10 C CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale17 C C ILE 12 C ILE 12 1_555 C N SAR 13 C SAR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 C C SAR 13 C SAR 13 1_555 C N CYS 14 C CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 D C ORN 1 D ORN 1 1_555 D N LYS 2 D LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale20 D NE ORN 1 D ORN 1 1_555 D C VAL 16 D VAL 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale21 D C GLU 8 D GLU 8 1_555 D NE ORN 9 D ORN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale22 D C ORN 9 D ORN 9 1_555 D N CYS 10 D CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale23 D C ILE 12 D ILE 12 1_555 D N SAR 13 D SAR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 D C SAR 13 D SAR 13 1_555 D N CYS 14 D CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale25 E C ORN 1 E ORN 1 1_555 E N LYS 2 E LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale26 E NE ORN 1 E ORN 1 1_555 E C VAL 16 E VAL 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale27 E C GLU 8 E GLU 8 1_555 E NE ORN 9 E ORN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale28 E C ORN 9 E ORN 9 1_555 E N CYS 10 E CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale29 E C ILE 12 E ILE 12 1_555 E N SAR 13 E SAR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale30 E C SAR 13 E SAR 13 1_555 E N CYS 14 E CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale31 F C ORN 1 F ORN 1 1_555 F N LYS 2 F LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale32 F NE ORN 1 F ORN 1 1_555 F C VAL 16 F VAL 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale33 F C GLU 8 F GLU 8 1_555 F NE ORN 9 F ORN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? covale ? covale34 F C ORN 9 F ORN 9 1_555 F N CYS 10 F CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale35 F C ILE 12 F ILE 12 1_555 F N SAR 13 F SAR 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale36 F C SAR 13 F SAR 13 1_555 F N CYS 14 F CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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 131 n n C1 H11 MPD sing 132 n n C1 H12 MPD sing 133 n n C1 H13 MPD sing 134 n n C2 O2 MPD sing 135 n n C2 CM MPD sing 136 n n C2 C3 MPD sing 137 n n O2 HO2 MPD sing 138 n n CM HM1 MPD sing 139 n n CM HM2 MPD sing 140 n n CM HM3 MPD sing 141 n n C3 C4 MPD sing 142 n n C3 H31 MPD sing 143 n n C3 H32 MPD sing 144 n n C4 O4 MPD sing 145 n n C4 C5 MPD sing 146 n n C4 H4 MPD sing 147 n n O4 HO4 MPD sing 148 n n C5 H51 MPD sing 149 n n C5 H52 MPD sing 150 n n C5 H53 MPD sing 151 n n # _atom_sites.entry_id 8ECA _atom_sites.fract_transf_matrix[1][1] 0.022969 _atom_sites.fract_transf_matrix[1][2] 0.013261 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026522 _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] 0.010715 _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 G 2 MPD A 1 101 1 MPD MPD . H 2 MPD D 1 101 2 MPD MPD . I 2 MPD D 1 102 3 MPD MPD . J 3 CL E 1 101 1 CL CL . K 2 MPD F 1 101 4 MPD MPD . L 4 HOH A 1 201 15 HOH HOH . L 4 HOH A 2 202 26 HOH HOH . L 4 HOH A 3 203 25 HOH HOH . L 4 HOH A 4 204 21 HOH HOH . M 4 HOH B 1 101 7 HOH HOH . M 4 HOH B 2 102 14 HOH HOH . N 4 HOH C 1 101 12 HOH HOH . N 4 HOH C 2 102 17 HOH HOH . O 4 HOH D 1 201 22 HOH HOH . O 4 HOH D 2 202 27 HOH HOH . O 4 HOH D 3 203 18 HOH HOH . O 4 HOH D 4 204 23 HOH HOH . O 4 HOH D 5 205 24 HOH HOH . P 4 HOH E 1 201 20 HOH HOH . P 4 HOH E 2 202 1 HOH HOH . P 4 HOH E 3 203 11 HOH HOH . Q 4 HOH F 1 201 2 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 . . . K 2 -21.955 -2.435 -17.873 1 76.37 ? C1 MPD 101 F 1 HETATM 2 C C2 MPD . . . K 2 -21.321 -1.465 -18.863 1 70.63 ? C2 MPD 101 F 1 HETATM 3 O O2 MPD . . . K 2 -19.889 -1.681 -18.887 1 83 ? O2 MPD 101 F 1 HETATM 4 C CM MPD . . . K 2 -21.854 -1.746 -20.265 1 83.83 ? CM MPD 101 F 1 HETATM 5 C C3 MPD . . . K 2 -21.631 -0.031 -18.444 1 69.72 ? C3 MPD 101 F 1 HETATM 6 C C4 MPD . . . K 2 -20.708 0.439 -17.322 1 67.45 ? C4 MPD 101 F 1 HETATM 7 O O4 MPD . . . K 2 -19.973 -0.648 -16.802 1 59.86 ? O4 MPD 101 F 1 HETATM 8 C C5 MPD . . . K 2 -19.738 1.508 -17.817 1 48.12 ? C5 MPD 101 F 1 HETATM 9 H H11 MPD . . . K 2 -22.741 -1.924 -17.316 1 92.69 ? H11 MPD 101 F 1 HETATM 10 H H12 MPD . . . K 2 -21.195 -2.796 -17.18 1 92.69 ? H12 MPD 101 F 1 HETATM 11 H H13 MPD . . . K 2 -22.383 -3.279 -18.414 1 92.69 ? H13 MPD 101 F 1 HETATM 12 H HO2 MPD . . . K 2 -19.431 -0.82 -18.985 1 100.64 ? HO2 MPD 101 F 1 HETATM 13 H HM1 MPD . . . K 2 -22.856 -2.168 -20.195 1 101.64 ? HM1 MPD 101 F 1 HETATM 14 H HM2 MPD . . . K 2 -21.196 -2.453 -20.769 1 101.64 ? HM2 MPD 101 F 1 HETATM 15 H HM3 MPD . . . K 2 -21.891 -0.816 -20.832 1 101.64 ? HM3 MPD 101 F 1 HETATM 16 H H31 MPD . . . K 2 -21.517 0.628 -19.305 1 84.72 ? H31 MPD 101 F 1 HETATM 17 H H32 MPD . . . K 2 -22.666 0.031 -18.109 1 84.72 ? H32 MPD 101 F 1 HETATM 18 H H4 MPD . . . K 2 -21.333 0.864 -16.536 1 81.99 ? H4 MPD 101 F 1 HETATM 19 H HO4 MPD . . . K 2 -19.032 -0.566 -17.065 1 72.88 ? HO4 MPD 101 F 1 HETATM 20 H H51 MPD . . . K 2 -20.223 2.483 -17.781 1 58.79 ? H51 MPD 101 F 1 HETATM 21 H H52 MPD . . . K 2 -19.445 1.286 -18.843 1 58.79 ? H52 MPD 101 F 1 HETATM 22 H H53 MPD . . . K 2 -18.854 1.518 -17.18 1 58.79 ? H53 MPD 101 F 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #