data_4Y13 # _model_server_result.job_id WJL6M0R3EXxr2y_Lph73HA _model_server_result.datetime_utc '2024-11-24 04:59:28' _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 4y13 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":305}' # _entry.id 4Y13 # _exptl.entry_id 4Y13 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _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 4Y13 _cell.length_a 129.857 _cell.length_b 129.857 _cell.length_c 125.68 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y13 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 12_565 x,x-y+1,-z+5/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -64.9285 112.459461 104.733333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N GLN 2 A GLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C THR 12 A THR 12 1_555 A N MSE 13 A MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C MSE 13 A MSE 13 1_555 A N LEU 14 A LEU 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C ARG 19 A ARG 19 1_555 A N MSE 20 A MSE 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C MSE 20 A MSE 20 1_555 A N GLU 21 A GLU 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C LEU 93 A LEU 93 1_555 A N MSE 94 A MSE 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C MSE 94 A MSE 94 1_555 A N TRP 95 A TRP 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C LEU 123 A LEU 123 1_555 A N MSE 124 A MSE 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 A C MSE 124 A MSE 124 1_555 A N LEU 125 A LEU 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C LYS 153 A LYS 153 1_555 A N MSE 154 A MSE 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C MSE 154 A MSE 154 1_555 A N GLN 155 A GLN 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale12 A C LEU 162 A LEU 162 1_555 A N MSE 163 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 A C MSE 163 A MSE 163 1_555 A N ALA 164 A ALA 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 A C LEU 165 A LEU 165 1_555 A N MSE 166 A MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale15 A C MSE 166 A MSE 166 1_555 A N ARG 167 A ARG 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 A C VAL 173 A VAL 173 1_555 A N MSE 174 A MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale17 A C MSE 174 A MSE 174 1_555 A N THR 175 A THR 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 A C GLU 177 A GLU 177 1_555 A N MSE 178 A MSE 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale19 A C MSE 178 A MSE 178 1_555 A N ASN 179 A ASN 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 A C ALA 201 A ALA 201 1_555 A N MSE 202 A MSE 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale21 A C MSE 202 A MSE 202 1_555 A N ILE 203 A ILE 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale22 A C ASN 217 A ASN 217 1_555 A N MSE 218 A MSE 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale23 A C MSE 218 A MSE 218 1_555 A N GLN 219 A GLN 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 165 n n C1 C2 GOL sing 166 n n C1 H11 GOL sing 167 n n C1 H12 GOL sing 168 n n O1 HO1 GOL sing 169 n n C2 O2 GOL sing 170 n n C2 C3 GOL sing 171 n n C2 H2 GOL sing 172 n n O2 HO2 GOL sing 173 n n C3 O3 GOL sing 174 n n C3 H31 GOL sing 175 n n C3 H32 GOL sing 176 n n O3 HO3 GOL sing 177 n n # _atom_sites.entry_id 4Y13 _atom_sites.fract_transf_matrix[1][1] 0.007701 _atom_sites.fract_transf_matrix[1][2] 0.004446 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008892 _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] 0.007957 _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 B 2 SO4 A 1 301 301 SO4 SO4 . C 2 SO4 A 1 302 302 SO4 SO4 . D 3 480 A 1 303 501 480 OLC . E 4 GOL A 1 304 601 GOL GOL . F 4 GOL A 1 305 602 GOL GOL . G 5 HOH A 1 401 401 HOH HOH . G 5 HOH A 2 402 402 HOH HOH . G 5 HOH A 3 403 403 HOH HOH . G 5 HOH A 4 404 404 HOH HOH . G 5 HOH A 5 405 405 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 GOL . . . F 4 17.078 62.171 45.3 1 92.14 ? C1 GOL 305 A 1 HETATM 2 O O1 GOL . . . F 4 18.231 61.541 45.713 1 83.03 ? O1 GOL 305 A 1 HETATM 3 C C2 GOL . . . F 4 16.158 61.181 44.678 1 105.87 ? C2 GOL 305 A 1 HETATM 4 O O2 GOL . . . F 4 16.849 60.377 43.796 1 108.74 ? O2 GOL 305 A 1 HETATM 5 C C3 GOL . . . F 4 15.588 60.328 45.754 1 103.23 ? C3 GOL 305 A 1 HETATM 6 O O3 GOL . . . F 4 16.629 59.687 46.394 1 98.36 ? O3 GOL 305 A 1 HETATM 7 H H11 GOL . . . F 4 17.272 62.892 44.677 1 110.56 ? H11 GOL 305 A 1 HETATM 8 H H12 GOL . . . F 4 16.647 62.537 46.092 1 110.56 ? H12 GOL 305 A 1 HETATM 9 H HO1 GOL . . . F 4 18.895 61.751 45.165 1 99.64 ? HO1 GOL 305 A 1 HETATM 10 H H2 GOL . . . F 4 15.441 61.637 44.207 1 127.04 ? H2 GOL 305 A 1 HETATM 11 H HO2 GOL . . . F 4 16.434 59.598 43.719 1 130.49 ? HO2 GOL 305 A 1 HETATM 12 H H31 GOL . . . F 4 14.99 59.668 45.365 1 123.87 ? H31 GOL 305 A 1 HETATM 13 H H32 GOL . . . F 4 15.099 60.881 46.388 1 123.87 ? H32 GOL 305 A 1 HETATM 14 H HO3 GOL . . . F 4 17.014 59.119 45.835 1 118.03 ? HO3 GOL 305 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #