data_2YQ6 # _model_server_result.job_id OyNe1jVM3xvarJOvFrP8-A _model_server_result.datetime_utc '2024-12-08 16:16:20' _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 2yq6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1198}' # _entry.id 2YQ6 # _exptl.entry_id 2YQ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.61 _cell.angle_gamma 90 _cell.entry_id 2YQ6 _cell.length_a 73.736 _cell.length_b 35.336 _cell.length_c 61.412 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YQ6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 2_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 11.307356 0 -60.362053 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I 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 B C ARG 7 B ARG 153 1_555 B N MK8 8 B MK8 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 B C MK8 8 B MK8 154 1_555 B N ILE 9 B ILE 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 B CE MK8 8 B MK8 154 1_555 B CE MK8 12 B MK8 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale4 B C ASP 11 B ASP 157 1_555 B N MK8 12 B MK8 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 B C MK8 12 B MK8 158 1_555 B N PHE 13 B PHE 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C ALA 18 B ALA 164 1_555 B N NH2 19 B NH2 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 2YQ6 _atom_sites.fract_transf_matrix[1][1] 0.013562 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00254 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0283 _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] 0.016567 _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 3 GOL A 1 1197 1197 GOL GOL . D 3 GOL A 1 1198 1198 GOL GOL . E 3 GOL A 1 1199 1199 GOL GOL . F 3 GOL A 1 1200 1200 GOL GOL . G 3 GOL A 1 1201 1201 GOL GOL . H 3 GOL A 1 1202 1202 GOL GOL . I 3 GOL B 1 1000 1000 GOL GOL . J 4 HOH A 1 2001 2001 HOH HOH . J 4 HOH A 2 2002 2002 HOH HOH . J 4 HOH A 3 2003 2003 HOH HOH . J 4 HOH A 4 2004 2004 HOH HOH . J 4 HOH A 5 2005 2005 HOH HOH . J 4 HOH A 6 2006 2006 HOH HOH . J 4 HOH A 7 2007 2007 HOH HOH . J 4 HOH A 8 2008 2008 HOH HOH . J 4 HOH A 9 2009 2009 HOH HOH . J 4 HOH A 10 2010 2010 HOH HOH . J 4 HOH A 11 2011 2011 HOH HOH . J 4 HOH A 12 2012 2012 HOH HOH . J 4 HOH A 13 2013 2013 HOH HOH . J 4 HOH A 14 2014 2014 HOH HOH . J 4 HOH A 15 2015 2015 HOH HOH . J 4 HOH A 16 2016 2016 HOH HOH . J 4 HOH A 17 2017 2017 HOH HOH . J 4 HOH A 18 2018 2018 HOH HOH . J 4 HOH A 19 2019 2019 HOH HOH . J 4 HOH A 20 2020 2020 HOH HOH . J 4 HOH A 21 2021 2021 HOH HOH . J 4 HOH A 22 2022 2022 HOH HOH . J 4 HOH A 23 2023 2023 HOH HOH . J 4 HOH A 24 2024 2024 HOH HOH . J 4 HOH A 25 2025 2025 HOH HOH . J 4 HOH A 26 2026 2026 HOH HOH . J 4 HOH A 27 2027 2027 HOH HOH . J 4 HOH A 28 2028 2028 HOH HOH . J 4 HOH A 29 2029 2029 HOH HOH . J 4 HOH A 30 2030 2030 HOH HOH . J 4 HOH A 31 2031 2031 HOH HOH . J 4 HOH A 32 2032 2032 HOH HOH . J 4 HOH A 33 2033 2033 HOH HOH . J 4 HOH A 34 2034 2034 HOH HOH . J 4 HOH A 35 2035 2035 HOH HOH . J 4 HOH A 36 2036 2036 HOH HOH . J 4 HOH A 37 2037 2037 HOH HOH . J 4 HOH A 38 2038 2038 HOH HOH . J 4 HOH A 39 2039 2039 HOH HOH . J 4 HOH A 40 2040 2040 HOH HOH . J 4 HOH A 41 2041 2041 HOH HOH . J 4 HOH A 42 2042 2042 HOH HOH . J 4 HOH A 43 2043 2043 HOH HOH . J 4 HOH A 44 2044 2044 HOH HOH . J 4 HOH A 45 2045 2045 HOH HOH . J 4 HOH A 46 2046 2046 HOH HOH . J 4 HOH A 47 2047 2047 HOH HOH . J 4 HOH A 48 2048 2048 HOH HOH . J 4 HOH A 49 2049 2049 HOH HOH . J 4 HOH A 50 2050 2050 HOH HOH . J 4 HOH A 51 2051 2051 HOH HOH . J 4 HOH A 52 2052 2052 HOH HOH . J 4 HOH A 53 2053 2053 HOH HOH . J 4 HOH A 54 2054 2054 HOH HOH . J 4 HOH A 55 2055 2055 HOH HOH . J 4 HOH A 56 2056 2056 HOH HOH . J 4 HOH A 57 2057 2057 HOH HOH . J 4 HOH A 58 2058 2058 HOH HOH . J 4 HOH A 59 2059 2059 HOH HOH . J 4 HOH A 60 2060 2060 HOH HOH . J 4 HOH A 61 2061 2061 HOH HOH . J 4 HOH A 62 2062 2062 HOH HOH . J 4 HOH A 63 2063 2063 HOH HOH . J 4 HOH A 64 2064 2064 HOH HOH . J 4 HOH A 65 2065 2065 HOH HOH . J 4 HOH A 66 2066 2066 HOH HOH . J 4 HOH A 67 2067 2067 HOH HOH . J 4 HOH A 68 2068 2068 HOH HOH . J 4 HOH A 69 2069 2069 HOH HOH . K 4 HOH B 1 2001 2001 HOH HOH . K 4 HOH B 2 2002 2002 HOH HOH . K 4 HOH B 3 2003 2003 HOH HOH . K 4 HOH B 4 2004 2004 HOH HOH . K 4 HOH B 5 2005 2005 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 . . . D 3 -5.487 1.464 -7.63 1 26.25 ? C1 GOL 1198 A 1 HETATM 2 O O1 GOL . . . D 3 -4.182 1.589 -8.166 1 21.93 ? O1 GOL 1198 A 1 HETATM 3 C C2 GOL . . . D 3 -5.411 1.35 -6.107 1 29.66 ? C2 GOL 1198 A 1 HETATM 4 O O2 GOL . . . D 3 -4.837 2.525 -5.59 1 25.36 ? O2 GOL 1198 A 1 HETATM 5 C C3 GOL . . . D 3 -6.819 1.219 -5.536 1 37.38 ? C3 GOL 1198 A 1 HETATM 6 O O3 GOL . . . D 3 -7.374 0.002 -5.976 1 53.84 ? O3 GOL 1198 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #