data_2BNF # _model_server_result.job_id 6xaMRdr6VEFhXJUn3YFrzQ _model_server_result.datetime_utc '2025-03-04 15:25:16' _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 2bnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1245}' # _entry.id 2BNF # _exptl.entry_id 2BNF _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 90 _cell.angle_gamma 120 _cell.entry_id 2BNF _cell.length_a 141.91 _cell.length_b 141.91 _cell.length_c 60.38 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BNF _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 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 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 J N N ? 3 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 covale ? covale1 A C ARG 36 A ARG 36 1_555 A N MSE 37 A MSE 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 37 A MSE 37 1_555 A N ALA 38 A ALA 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C GLY 70 A GLY 70 1_555 A N MSE 71 A MSE 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 A C MSE 71 A MSE 71 1_555 A N ASN 72 A ASN 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C HIS 78 A HIS 78 1_555 A N MSE 79 A MSE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C MSE 79 A MSE 79 1_555 A N GLY 80 A GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A C GLY 80 A GLY 80 1_555 A N MSE 81 A MSE 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 81 A MSE 81 1_555 A N LEU 82 A LEU 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale9 A C VAL 85 A VAL 85 1_555 A N MSE 86 A MSE 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 A C MSE 86 A MSE 86 1_555 A N ASN 87 A ASN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale11 A C ALA 90 A ALA 90 1_555 A N MSE 91 A MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 A C MSE 91 A MSE 91 1_555 A N ARG 92 A ARG 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 A C LEU 104 A LEU 104 1_555 A N MSE 105 A MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 A C MSE 105 A MSE 105 1_555 A N SER 106 A SER 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 A C THR 182 A THR 182 1_555 A N MSE 183 A MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale16 A C MSE 183 A MSE 183 1_555 A N TYR 184 A TYR 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 A C VAL 199 A VAL 199 1_555 A N MSE 200 A MSE 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale18 A C MSE 200 A MSE 200 1_555 A N ASP 201 A ASP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale19 A C ASN 219 A ASN 219 1_555 A N MSE 220 A MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 A C MSE 220 A MSE 220 1_555 A N ASN 221 A ASN 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale21 A C VAL 230 A VAL 230 1_555 A N MSE 231 A MSE 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 A C MSE 231 A MSE 231 1_555 A N GLY 232 A GLY 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 B C ARG 36 B ARG 36 1_555 B N MSE 37 B MSE 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale24 B C MSE 37 B MSE 37 1_555 B N ALA 38 B ALA 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale25 B C GLY 70 B GLY 70 1_555 B N MSE 71 B MSE 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale26 B C MSE 71 B MSE 71 1_555 B N ASN 72 B ASN 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale27 B C HIS 78 B HIS 78 1_555 B N MSE 79 B MSE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale28 B C MSE 79 B MSE 79 1_555 B N GLY 80 B GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale29 B C GLY 80 B GLY 80 1_555 B N MSE 81 B MSE 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale30 B C MSE 81 B MSE 81 1_555 B N LEU 82 B LEU 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale31 B C VAL 85 B VAL 85 1_555 B N MSE 86 B MSE 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale32 B C MSE 86 B MSE 86 1_555 B N ASN 87 B ASN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale33 B C ALA 90 B ALA 90 1_555 B N MSE 91 B MSE 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale34 B C MSE 91 B MSE 91 1_555 B N ARG 92 B ARG 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale35 B C LEU 104 B LEU 104 1_555 B N MSE 105 B MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale36 B C MSE 105 B MSE 105 1_555 B N SER 106 B SER 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale37 B C THR 182 B THR 182 1_555 B N MSE 183 B MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale38 B C MSE 183 B MSE 183 1_555 B N TYR 184 B TYR 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale39 B C VAL 199 B VAL 199 1_555 B N MSE 200 B MSE 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale40 B C MSE 200 B MSE 200 1_555 B N ASP 201 B ASP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale41 B C ASN 219 B ASN 219 1_555 B N MSE 220 B MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale42 B C MSE 220 B MSE 220 1_555 B N ASN 221 B ASN 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale43 B C VAL 230 B VAL 230 1_555 B N MSE 231 B MSE 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale44 B C MSE 231 B MSE 231 1_555 B N GLY 232 B GLY 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _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 2BNF _atom_sites.fract_transf_matrix[1][1] 0.007047 _atom_sites.fract_transf_matrix[1][2] 0.004068 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008137 _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] 0.016562 _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 UTP A 1 1242 1242 UTP UTP . D 3 GOL A 1 1243 1243 GOL GOL . E 3 GOL A 1 1244 1244 GOL GOL . F 3 GOL A 1 1245 1245 GOL GOL . G 3 GOL A 1 1246 1246 GOL GOL . H 3 GOL A 1 1247 1247 GOL GOL . I 2 UTP B 1 1242 1242 UTP UTP . J 3 GOL B 1 1243 1243 GOL GOL . K 3 GOL B 1 1244 1244 GOL GOL . L 4 HOH A 1 2001 2001 HOH HOH . L 4 HOH A 2 2002 2002 HOH HOH . L 4 HOH A 3 2003 2003 HOH HOH . L 4 HOH A 4 2004 2004 HOH HOH . L 4 HOH A 5 2005 2005 HOH HOH . L 4 HOH A 6 2006 2006 HOH HOH . L 4 HOH A 7 2007 2007 HOH HOH . L 4 HOH A 8 2008 2008 HOH HOH . L 4 HOH A 9 2009 2009 HOH HOH . L 4 HOH A 10 2010 2010 HOH HOH . L 4 HOH A 11 2011 2011 HOH HOH . L 4 HOH A 12 2012 2012 HOH HOH . L 4 HOH A 13 2013 2013 HOH HOH . L 4 HOH A 14 2014 2014 HOH HOH . L 4 HOH A 15 2015 2015 HOH HOH . L 4 HOH A 16 2016 2016 HOH HOH . L 4 HOH A 17 2017 2017 HOH HOH . L 4 HOH A 18 2018 2018 HOH HOH . L 4 HOH A 19 2019 2019 HOH HOH . L 4 HOH A 20 2020 2020 HOH HOH . L 4 HOH A 21 2021 2021 HOH HOH . L 4 HOH A 22 2022 2022 HOH HOH . L 4 HOH A 23 2023 2023 HOH HOH . L 4 HOH A 24 2024 2024 HOH HOH . L 4 HOH A 25 2025 2025 HOH HOH . L 4 HOH A 26 2026 2026 HOH HOH . L 4 HOH A 27 2027 2027 HOH HOH . L 4 HOH A 28 2028 2028 HOH HOH . L 4 HOH A 29 2029 2029 HOH HOH . L 4 HOH A 30 2030 2030 HOH HOH . L 4 HOH A 31 2031 2031 HOH HOH . L 4 HOH A 32 2032 2032 HOH HOH . L 4 HOH A 33 2033 2033 HOH HOH . L 4 HOH A 34 2034 2034 HOH HOH . L 4 HOH A 35 2035 2035 HOH HOH . L 4 HOH A 36 2036 2036 HOH HOH . L 4 HOH A 37 2037 2037 HOH HOH . L 4 HOH A 38 2038 2038 HOH HOH . L 4 HOH A 39 2039 2039 HOH HOH . L 4 HOH A 40 2040 2040 HOH HOH . L 4 HOH A 41 2041 2041 HOH HOH . M 4 HOH B 1 2001 2001 HOH HOH . M 4 HOH B 2 2002 2002 HOH HOH . M 4 HOH B 3 2003 2003 HOH HOH . M 4 HOH B 4 2004 2004 HOH HOH . M 4 HOH B 5 2005 2005 HOH HOH . M 4 HOH B 6 2006 2006 HOH HOH . M 4 HOH B 7 2007 2007 HOH HOH . M 4 HOH B 8 2008 2008 HOH HOH . M 4 HOH B 9 2009 2009 HOH HOH . M 4 HOH B 10 2010 2010 HOH HOH . M 4 HOH B 11 2011 2011 HOH HOH . M 4 HOH B 12 2012 2012 HOH HOH . M 4 HOH B 13 2013 2013 HOH HOH . M 4 HOH B 14 2014 2014 HOH HOH . M 4 HOH B 15 2015 2015 HOH HOH . M 4 HOH B 16 2016 2016 HOH HOH . M 4 HOH B 17 2017 2017 HOH HOH . M 4 HOH B 18 2018 2018 HOH HOH . M 4 HOH B 19 2019 2019 HOH HOH . M 4 HOH B 20 2020 2020 HOH HOH . M 4 HOH B 21 2021 2021 HOH HOH . M 4 HOH B 22 2022 2022 HOH HOH . M 4 HOH B 23 2023 2023 HOH HOH . M 4 HOH B 24 2024 2024 HOH HOH . M 4 HOH B 25 2025 2025 HOH HOH . M 4 HOH B 26 2026 2026 HOH HOH . M 4 HOH B 27 2027 2027 HOH HOH . M 4 HOH B 28 2028 2028 HOH HOH . M 4 HOH B 29 2029 2029 HOH HOH . M 4 HOH B 30 2030 2030 HOH HOH . M 4 HOH B 31 2031 2031 HOH HOH . M 4 HOH B 32 2032 2032 HOH HOH . M 4 HOH B 33 2033 2033 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 3 -31.013 -1.167 -29.858 1 47.49 ? C1 GOL 1245 A 1 HETATM 2 O O1 GOL . . . F 3 -31.569 -2.374 -30.386 1 43.72 ? O1 GOL 1245 A 1 HETATM 3 C C2 GOL . . . F 3 -30.122 -1.35 -28.612 1 49.7 ? C2 GOL 1245 A 1 HETATM 4 O O2 GOL . . . F 3 -29.86 -2.713 -28.293 1 52.23 ? O2 GOL 1245 A 1 HETATM 5 C C3 GOL . . . F 3 -30.757 -0.678 -27.39 1 50.63 ? C3 GOL 1245 A 1 HETATM 6 O O3 GOL . . . F 3 -29.976 -0.994 -26.239 1 50 ? O3 GOL 1245 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #