data_2VNJ # _model_server_result.job_id W1PvvS7lmhYhS4BE-bDNqA _model_server_result.datetime_utc '2024-11-29 16:07:03' _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 2vnj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":275}' # _entry.id 2VNJ # _exptl.entry_id 2VNJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 294.408 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'heptyl 1-thio-beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 1 _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 2VNJ _cell.length_a 68.72 _cell.length_b 68.72 _cell.length_c 128.15 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VNJ _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 PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C13 H26 O5 S' _chem_comp.formula_weight 294.408 _chem_comp.id HTG _chem_comp.mon_nstd_flag . _chem_comp.name 'heptyl 1-thio-beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'HEPTYL 1-THIOHEXOPYRANOSIDE;heptyl 1-thio-beta-D-glucoside;heptyl 1-thio-D-glucoside;heptyl 1-thio-glucoside' # 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 S1 HTG sing 243 n n C1 C2 HTG sing 244 n n C1 O5 HTG sing 245 n n C1 H1 HTG sing 246 n n S1 C1' HTG sing 247 n n C2 O2 HTG sing 248 n n C2 C3 HTG sing 249 n n C2 H2 HTG sing 250 n n O2 HO2 HTG sing 251 n n C3 O3 HTG sing 252 n n C3 C4 HTG sing 253 n n C3 H3 HTG sing 254 n n O3 HO3 HTG sing 255 n n C4 O4 HTG sing 256 n n C4 C5 HTG sing 257 n n C4 H4 HTG sing 258 n n O4 HO4 HTG sing 259 n n C5 O5 HTG sing 260 n n C5 C6 HTG sing 261 n n C5 H5 HTG sing 262 n n C6 O6 HTG sing 263 n n C6 H61 HTG sing 264 n n C6 H62 HTG sing 265 n n O6 HO6 HTG sing 266 n n C1' C2' HTG sing 267 n n C1' "H1'1" HTG sing 268 n n C1' "H1'2" HTG sing 269 n n C2' C3' HTG sing 270 n n C2' "H2'1" HTG sing 271 n n C2' "H2'2" HTG sing 272 n n C3' C4' HTG sing 273 n n C3' "H3'1" HTG sing 274 n n C3' "H3'2" HTG sing 275 n n C4' C5' HTG sing 276 n n C4' "H4'1" HTG sing 277 n n C4' "H4'2" HTG sing 278 n n C5' C6' HTG sing 279 n n C5' "H5'1" HTG sing 280 n n C5' "H5'2" HTG sing 281 n n C6' C7' HTG sing 282 n n C6' "H6'1" HTG sing 283 n n C6' "H6'2" HTG sing 284 n n C7' "H7'1" HTG sing 285 n n C7' "H7'2" HTG sing 286 n n C7' "H7'3" HTG sing 287 n n # _atom_sites.entry_id 2VNJ _atom_sites.fract_transf_matrix[1][1] 0.014552 _atom_sites.fract_transf_matrix[1][2] 0.008401 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016803 _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] 0.007803 _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 FAD A 1 273 273 FAD FAD . C 3 NAP A 1 274 274 NAP NAP . D 4 HTG A 1 275 275 HTG HTG . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 HOH HOH . E 5 HOH A 82 2082 2082 HOH HOH . E 5 HOH A 83 2083 2083 HOH HOH . E 5 HOH A 84 2084 2084 HOH HOH . E 5 HOH A 85 2085 2085 HOH HOH . E 5 HOH A 86 2086 2086 HOH HOH . E 5 HOH A 87 2087 2087 HOH HOH . E 5 HOH A 88 2088 2088 HOH HOH . E 5 HOH A 89 2089 2089 HOH HOH . E 5 HOH A 90 2090 2090 HOH HOH . E 5 HOH A 91 2091 2091 HOH HOH . E 5 HOH A 92 2092 2092 HOH HOH . E 5 HOH A 93 2093 2093 HOH HOH . E 5 HOH A 94 2094 2094 HOH HOH . E 5 HOH A 95 2095 2095 HOH HOH . E 5 HOH A 96 2096 2096 HOH HOH . E 5 HOH A 97 2097 2097 HOH HOH . E 5 HOH A 98 2098 2098 HOH HOH . E 5 HOH A 99 2099 2099 HOH HOH . E 5 HOH A 100 2100 2100 HOH HOH . E 5 HOH A 101 2101 2101 HOH HOH . E 5 HOH A 102 2102 2102 HOH HOH . E 5 HOH A 103 2103 2103 HOH HOH . E 5 HOH A 104 2104 2104 HOH HOH . E 5 HOH A 105 2105 2105 HOH HOH . E 5 HOH A 106 2106 2106 HOH HOH . E 5 HOH A 107 2107 2107 HOH HOH . E 5 HOH A 108 2108 2108 HOH HOH . E 5 HOH A 109 2109 2109 HOH HOH . E 5 HOH A 110 2110 2110 HOH HOH . E 5 HOH A 111 2111 2111 HOH HOH . E 5 HOH A 112 2112 2112 HOH HOH . E 5 HOH A 113 2113 2113 HOH HOH . E 5 HOH A 114 2114 2114 HOH HOH . E 5 HOH A 115 2115 2115 HOH HOH . E 5 HOH A 116 2116 2116 HOH HOH . E 5 HOH A 117 2117 2117 HOH HOH . E 5 HOH A 118 2118 2118 HOH HOH . E 5 HOH A 119 2119 2119 HOH HOH . E 5 HOH A 120 2120 2120 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 HTG . . . D 4 3.064 10.452 12.065 1 65.26 ? C1 HTG 275 A 1 HETATM 2 S S1 HTG . . . D 4 3.012 12.283 12.294 1 66.65 ? S1 HTG 275 A 1 HETATM 3 C C2 HTG . . . D 4 3.516 9.977 10.647 1 64.74 ? C2 HTG 275 A 1 HETATM 4 O O2 HTG . . . D 4 2.768 10.681 9.683 1 64.94 ? O2 HTG 275 A 1 HETATM 5 C C3 HTG . . . D 4 3.255 8.449 10.585 1 64.5 ? C3 HTG 275 A 1 HETATM 6 O O3 HTG . . . D 4 3.625 7.891 9.331 1 65.12 ? O3 HTG 275 A 1 HETATM 7 C C4 HTG . . . D 4 4.1 7.746 11.667 1 64.41 ? C4 HTG 275 A 1 HETATM 8 O O4 HTG . . . D 4 3.821 6.353 11.597 1 64.39 ? O4 HTG 275 A 1 HETATM 9 C C5 HTG . . . D 4 3.717 8.323 13.082 1 64.28 ? C5 HTG 275 A 1 HETATM 10 O O5 HTG . . . D 4 3.786 9.756 13.094 1 64.7 ? O5 HTG 275 A 1 HETATM 11 C C6 HTG . . . D 4 4.623 7.868 14.259 1 63.74 ? C6 HTG 275 A 1 HETATM 12 O O6 HTG . . . D 4 5.983 8.33 14.098 1 60.74 ? O6 HTG 275 A 1 HETATM 13 C C1' HTG . . . D 4 2.822 12.473 14.059 1 67.6 ? C1' HTG 275 A 1 HETATM 14 C C2' HTG . . . D 4 1.426 12.735 14.621 1 67.52 ? C2' HTG 275 A 1 HETATM 15 C C3' HTG . . . D 4 0.757 11.424 15.142 1 68.62 ? C3' HTG 275 A 1 HETATM 16 C C4' HTG . . . D 4 0.422 11.274 16.663 1 67.67 ? C4' HTG 275 A 1 HETATM 17 C C5' HTG . . . D 4 -0.384 10.011 17.049 1 68.51 ? C5' HTG 275 A 1 HETATM 18 C C6' HTG . . . D 4 -1.401 9.528 15.99 1 68.07 ? C6' HTG 275 A 1 HETATM 19 C C7' HTG . . . D 4 -2.494 8.601 16.571 1 68.71 ? C7' HTG 275 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #