data_5FUW # _model_server_result.job_id DwvZAyqBnK1tzaltZzaPNg _model_server_result.datetime_utc '2024-11-23 14:19:43' _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 5fuw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1386}' # _entry.id 5FUW # _exptl.entry_id 5FUW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.224 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE' _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 90 _cell.entry_id 5FUW _cell.length_a 114.999 _cell.length_b 114.999 _cell.length_c 104.77 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FUW _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 2 2' # _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' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 123 A CYS 325 1_555 B SG CYS 123 B CYS 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc1 A SG CYS 139 A CYS 341 1_555 F ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc2 A SG CYS 142 A CYS 344 1_555 F ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc3 A SG CYS 172 A CYS 374 1_555 F ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc4 A SG CYS 175 A CYS 377 1_555 F ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 B SG CYS 139 B CYS 341 1_555 I ZN ZN . B ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc6 B SG CYS 142 B CYS 344 1_555 I ZN ZN . B ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc7 B SG CYS 172 B CYS 374 1_555 I ZN ZN . B ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc8 B SG CYS 175 B CYS 377 1_555 I ZN ZN . B ZN 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? # _chem_comp.formula 'C10 H17 N2 O8 P' _chem_comp.formula_weight 324.224 _chem_comp.id QBT _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE' _chem_comp.type 'dna linking' _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 P O1P QBT sing 281 n n P O2P QBT doub 282 n n P O5' QBT sing 283 n n P O3P QBT sing 284 n n O5' C5' QBT sing 285 n n C5' C4' QBT sing 286 n n C4' O4' QBT sing 287 n n C4' C3' QBT sing 288 n n O4' C1' QBT sing 289 n n C3' O3' QBT sing 290 n n C3' C2' QBT sing 291 n n C2' C1' QBT sing 292 n n C1' N1 QBT sing 293 n n N1 C2 QBT sing 294 n n N1 C6 QBT sing 295 n n C2 O2 QBT doub 296 n n C2 N3 QBT sing 297 n n N3 C4 QBT sing 298 n n C4 O4 QBT doub 299 n n C4 C5 QBT sing 300 n n C5 C5M QBT sing 301 n n O1P H1P QBT sing 302 n n C5' "H5'1" QBT sing 303 n n C5' "H5'2" QBT sing 304 n n C4' H4' QBT sing 305 n n C3' H3' QBT sing 306 n n C1' H1' QBT sing 307 n n O3' HA QBT sing 308 n n C2' "H2'1" QBT sing 309 n n C2' "H2'2" QBT sing 310 n n C6 H61C QBT sing 311 n n C6 H62C QBT sing 312 n n N3 H3 QBT sing 313 n n C5 C6 QBT sing 314 n n C5 H5M QBT sing 315 n n C5M H52 QBT sing 316 n n C5M H53 QBT sing 317 n n C5M H54 QBT sing 318 n n O3P H3P QBT sing 319 n n # _atom_sites.entry_id 5FUW _atom_sites.fract_transf_matrix[1][1] 0.008696 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008696 _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] 0.009545 _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 QBT A 1 1386 1386 QBT QBT . D 3 PO4 A 1 1387 1387 PO4 PO4 . E 3 PO4 A 1 1388 1388 PO4 PO4 . F 4 ZN A 1 1389 1389 ZN ZN . G 3 PO4 B 1 1385 1385 PO4 PO4 . H 5 THM B 1 1386 1386 THM THM . I 4 ZN B 1 1387 1387 ZN ZN . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH A 13 2013 2013 HOH HOH . J 6 HOH A 14 2014 2014 HOH HOH . J 6 HOH A 15 2015 2015 HOH HOH . J 6 HOH A 16 2016 2016 HOH HOH . J 6 HOH A 17 2017 2017 HOH HOH . J 6 HOH A 18 2018 2018 HOH HOH . J 6 HOH A 19 2019 2019 HOH HOH . J 6 HOH A 20 2020 2020 HOH HOH . J 6 HOH A 21 2021 2021 HOH HOH . J 6 HOH A 22 2022 2022 HOH HOH . J 6 HOH A 23 2023 2023 HOH HOH . J 6 HOH A 24 2024 2024 HOH HOH . J 6 HOH A 25 2025 2025 HOH HOH . J 6 HOH A 26 2026 2026 HOH HOH . J 6 HOH A 27 2027 2027 HOH HOH . J 6 HOH A 28 2028 2028 HOH HOH . J 6 HOH A 29 2029 2029 HOH HOH . J 6 HOH A 30 2030 2030 HOH HOH . J 6 HOH A 31 2031 2031 HOH HOH . J 6 HOH A 32 2032 2032 HOH HOH . J 6 HOH A 33 2033 2033 HOH HOH . J 6 HOH A 34 2034 2034 HOH HOH . J 6 HOH A 35 2035 2035 HOH HOH . J 6 HOH A 36 2036 2036 HOH HOH . J 6 HOH A 37 2037 2037 HOH HOH . J 6 HOH A 38 2038 2038 HOH HOH . J 6 HOH A 39 2039 2039 HOH HOH . J 6 HOH A 40 2040 2040 HOH HOH . J 6 HOH A 41 2041 2041 HOH HOH . J 6 HOH A 42 2042 2042 HOH HOH . J 6 HOH A 43 2043 2043 HOH HOH . J 6 HOH A 44 2044 2044 HOH HOH . J 6 HOH A 45 2045 2045 HOH HOH . J 6 HOH A 46 2046 2046 HOH HOH . J 6 HOH A 47 2047 2047 HOH HOH . J 6 HOH A 48 2048 2048 HOH HOH . J 6 HOH A 49 2049 2049 HOH HOH . J 6 HOH A 50 2050 2050 HOH HOH . J 6 HOH A 51 2051 2051 HOH HOH . J 6 HOH A 52 2052 2052 HOH HOH . J 6 HOH A 53 2053 2053 HOH HOH . J 6 HOH A 54 2054 2054 HOH HOH . J 6 HOH A 55 2055 2055 HOH HOH . J 6 HOH A 56 2056 2056 HOH HOH . J 6 HOH A 57 2057 2057 HOH HOH . J 6 HOH A 58 2058 2058 HOH HOH . J 6 HOH A 59 2059 2059 HOH HOH . J 6 HOH A 60 2060 2060 HOH HOH . J 6 HOH A 61 2061 2061 HOH HOH . J 6 HOH A 62 2062 2062 HOH HOH . J 6 HOH A 63 2063 2063 HOH HOH . J 6 HOH A 64 2064 2064 HOH HOH . J 6 HOH A 65 2065 2065 HOH HOH . J 6 HOH A 66 2066 2066 HOH HOH . J 6 HOH A 67 2067 2067 HOH HOH . J 6 HOH A 68 2068 2068 HOH HOH . J 6 HOH A 69 2069 2069 HOH HOH . J 6 HOH A 70 2070 2070 HOH HOH . J 6 HOH A 71 2071 2071 HOH HOH . J 6 HOH A 72 2072 2072 HOH HOH . J 6 HOH A 73 2073 2073 HOH HOH . J 6 HOH A 74 2074 2074 HOH HOH . J 6 HOH A 75 2075 2075 HOH HOH . J 6 HOH A 76 2076 2076 HOH HOH . J 6 HOH A 77 2077 2077 HOH HOH . J 6 HOH A 78 2078 2078 HOH HOH . J 6 HOH A 79 2079 2079 HOH HOH . J 6 HOH A 80 2080 2080 HOH HOH . J 6 HOH A 81 2081 2081 HOH HOH . J 6 HOH A 82 2082 2082 HOH HOH . J 6 HOH A 83 2083 2083 HOH HOH . J 6 HOH A 84 2084 2084 HOH HOH . J 6 HOH A 85 2085 2085 HOH HOH . J 6 HOH A 86 2086 2086 HOH HOH . J 6 HOH A 87 2087 2087 HOH HOH . J 6 HOH A 88 2088 2088 HOH HOH . J 6 HOH A 89 2089 2089 HOH HOH . J 6 HOH A 90 2090 2090 HOH HOH . J 6 HOH A 91 2091 2091 HOH HOH . J 6 HOH A 92 2092 2092 HOH HOH . J 6 HOH A 93 2093 2093 HOH HOH . J 6 HOH A 94 2094 2094 HOH HOH . J 6 HOH A 95 2095 2095 HOH HOH . J 6 HOH A 96 2096 2096 HOH HOH . J 6 HOH A 97 2097 2097 HOH HOH . J 6 HOH A 98 2098 2098 HOH HOH . J 6 HOH A 99 2099 2099 HOH HOH . J 6 HOH A 100 2100 2100 HOH HOH . J 6 HOH A 101 2101 2101 HOH HOH . J 6 HOH A 102 2102 2102 HOH HOH . J 6 HOH A 103 2103 2103 HOH HOH . J 6 HOH A 104 2104 2104 HOH HOH . J 6 HOH A 105 2105 2105 HOH HOH . J 6 HOH A 106 2106 2106 HOH HOH . J 6 HOH A 107 2107 2107 HOH HOH . K 6 HOH B 1 2001 2001 HOH HOH . K 6 HOH B 2 2002 2002 HOH HOH . K 6 HOH B 3 2003 2003 HOH HOH . K 6 HOH B 4 2004 2004 HOH HOH . K 6 HOH B 5 2005 2005 HOH HOH . K 6 HOH B 6 2006 2006 HOH HOH . K 6 HOH B 7 2007 2007 HOH HOH . K 6 HOH B 8 2008 2008 HOH HOH . K 6 HOH B 9 2009 2009 HOH HOH . K 6 HOH B 10 2010 2010 HOH HOH . K 6 HOH B 11 2011 2011 HOH HOH . K 6 HOH B 12 2012 2012 HOH HOH . K 6 HOH B 13 2013 2013 HOH HOH . K 6 HOH B 14 2014 2014 HOH HOH . K 6 HOH B 15 2015 2015 HOH HOH . K 6 HOH B 16 2016 2016 HOH HOH . K 6 HOH B 17 2017 2017 HOH HOH . K 6 HOH B 18 2018 2018 HOH HOH . K 6 HOH B 19 2019 2019 HOH HOH . K 6 HOH B 20 2020 2020 HOH HOH . K 6 HOH B 21 2021 2021 HOH HOH . K 6 HOH B 22 2022 2022 HOH HOH . K 6 HOH B 23 2023 2023 HOH HOH . K 6 HOH B 24 2024 2024 HOH HOH . K 6 HOH B 25 2025 2025 HOH HOH . K 6 HOH B 26 2026 2026 HOH HOH . K 6 HOH B 27 2027 2027 HOH HOH . K 6 HOH B 28 2028 2028 HOH HOH . K 6 HOH B 29 2029 2029 HOH HOH . K 6 HOH B 30 2030 2030 HOH HOH . K 6 HOH B 31 2031 2031 HOH HOH . K 6 HOH B 32 2032 2032 HOH HOH . K 6 HOH B 33 2033 2033 HOH HOH . K 6 HOH B 34 2034 2034 HOH HOH . K 6 HOH B 35 2035 2035 HOH HOH . K 6 HOH B 36 2036 2036 HOH HOH . K 6 HOH B 37 2037 2037 HOH HOH . K 6 HOH B 38 2038 2038 HOH HOH . K 6 HOH B 39 2039 2039 HOH HOH . K 6 HOH B 40 2040 2040 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 P P QBT . . . C 2 -10.418 -19.07 -9.412 0.5 74.78 ? P QBT 1386 A 1 HETATM 2 O O1P QBT . . . C 2 -9.264 -18.426 -10.045 0.5 63.28 ? O1P QBT 1386 A 1 HETATM 3 O O2P QBT . . . C 2 -10.441 -18.796 -7.905 0.5 43.17 ? O2P QBT 1386 A 1 HETATM 4 O O5' QBT . . . C 2 -11.618 -18.16 -10.127 1 60.58 ? O5' QBT 1386 A 1 HETATM 5 C C5' QBT . . . C 2 -12.344 -18.742 -11.142 1 45.59 ? C5' QBT 1386 A 1 HETATM 6 C C4' QBT . . . C 2 -12.909 -17.774 -12.128 1 42.29 ? C4' QBT 1386 A 1 HETATM 7 O O4' QBT . . . C 2 -13.645 -18.626 -13.025 1 44.08 ? O4' QBT 1386 A 1 HETATM 8 C C3' QBT . . . C 2 -13.903 -16.776 -11.582 1 39.37 ? C3' QBT 1386 A 1 HETATM 9 O O3' QBT . . . C 2 -13.695 -15.57 -12.36 1 41.26 ? O3' QBT 1386 A 1 HETATM 10 C C2' QBT . . . C 2 -15.269 -17.337 -11.888 1 40.52 ? C2' QBT 1386 A 1 HETATM 11 C C1' QBT . . . C 2 -14.969 -18.13 -13.089 1 41.85 ? C1' QBT 1386 A 1 HETATM 12 N N1 QBT . . . C 2 -15.816 -19.241 -13.286 1 44.91 ? N1 QBT 1386 A 1 HETATM 13 C C2 QBT . . . C 2 -16.498 -19.388 -14.529 1 45.11 ? C2 QBT 1386 A 1 HETATM 14 O O2 QBT . . . C 2 -16.324 -18.558 -15.438 1 41.21 ? O2 QBT 1386 A 1 HETATM 15 N N3 QBT . . . C 2 -17.244 -20.461 -14.754 1 40.88 ? N3 QBT 1386 A 1 HETATM 16 C C4 QBT . . . C 2 -17.486 -21.379 -13.83 1 42.55 ? C4 QBT 1386 A 1 HETATM 17 O O4 QBT . . . C 2 -18.2 -22.391 -14.019 1 42.18 ? O4 QBT 1386 A 1 HETATM 18 C C5 QBT . . . C 2 -16.747 -21.235 -12.535 1 38.99 ? C5 QBT 1386 A 1 HETATM 19 C C6 QBT . . . C 2 -15.966 -20.099 -12.326 1 42.2 ? C6 QBT 1386 A 1 HETATM 20 C C5M QBT . . . C 2 -17.002 -22.28 -11.516 1 38 ? C5M QBT 1386 A 1 HETATM 21 O O3P QBT . . . C 2 -10.344 -20.533 -9.849 0.5 48.39 ? O3P QBT 1386 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #