data_5FUX # _model_server_result.job_id dWLGt-S_Nik-gXx8RlllZQ _model_server_result.datetime_utc '2024-11-24 06:16:01' _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 5fux # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1388}' # _entry.id 5FUX # _exptl.entry_id 5FUX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.224 _entity.id 5 _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 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 90 _cell.entry_id 5FUX _cell.length_a 114.76 _cell.length_b 114.76 _cell.length_c 104.45 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FUX _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 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 disulf ? disulf1 A SG CYS 123 A CYS 325 1_555 B SG CYS 123 B CYS 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc1 A OG1 THR 17 A THR 219 1_555 C MG MG . A MG 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc2 A SG CYS 139 A CYS 341 1_555 D ZN ZN . A ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A SG CYS 142 A CYS 344 1_555 D ZN ZN . A ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 A SG CYS 172 A CYS 374 1_555 D ZN ZN . A ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 A SG CYS 175 A CYS 377 1_555 D ZN ZN . A ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc6 C MG MG . A MG 1385 1_555 E O2 PO4 . A PO4 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc7 C MG MG . A MG 1385 1_555 F O3P QBT . A QBT 1388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc8 C MG MG . A MG 1385 1_555 J O HOH . A HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc9 C MG MG . A MG 1385 1_555 J O HOH . A HOH 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc10 B SG CYS 139 B CYS 341 1_555 G ZN ZN . B ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc11 B SG CYS 142 B CYS 344 1_555 G ZN ZN . B ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc12 B SG CYS 172 B CYS 374 1_555 G ZN ZN . B ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc13 B SG CYS 175 B CYS 377 1_555 G ZN ZN . B ZN 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? # _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 5FUX _atom_sites.fract_transf_matrix[1][1] 0.008714 _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] 0.008714 _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] 0.009574 _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 MG A 1 1385 1385 MG MG . D 3 ZN A 1 1386 1386 ZN ZN . E 4 PO4 A 1 1387 1387 PO4 PO4 . F 5 QBT A 1 1388 1388 QBT QBT . G 3 ZN B 1 1385 1385 ZN ZN . H 4 PO4 B 1 1386 1386 PO4 PO4 . I 5 QBT B 1 1387 1387 QBT QBT . 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 . 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 . # 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 . . . F 5 -10.188 -19.688 -9.81 0.5 64.97 ? P QBT 1388 A 1 HETATM 2 O O1P QBT . . . F 5 -10.612 -20.517 -8.633 0.5 31.31 ? O1P QBT 1388 A 1 HETATM 3 O O2P QBT . . . F 5 -9.396 -20.479 -10.942 0.5 39.67 ? O2P QBT 1388 A 1 HETATM 4 O O5' QBT . . . F 5 -11.563 -19.259 -10.683 1 68.98 ? O5' QBT 1388 A 1 HETATM 5 C C5' QBT . . . F 5 -12.204 -18.062 -10.646 1 50.12 ? C5' QBT 1388 A 1 HETATM 6 C C4' QBT . . . F 5 -12.845 -17.603 -11.972 1 49.38 ? C4' QBT 1388 A 1 HETATM 7 O O4' QBT . . . F 5 -13.524 -18.545 -12.757 1 48.2 ? O4' QBT 1388 A 1 HETATM 8 C C3' QBT . . . F 5 -13.927 -16.586 -11.582 1 47.68 ? C3' QBT 1388 A 1 HETATM 9 O O3' QBT . . . F 5 -13.696 -15.456 -12.393 1 48.28 ? O3' QBT 1388 A 1 HETATM 10 C C2' QBT . . . F 5 -15.274 -17.176 -11.934 1 44.21 ? C2' QBT 1388 A 1 HETATM 11 C C1' QBT . . . F 5 -14.867 -18.044 -13.055 1 49.78 ? C1' QBT 1388 A 1 HETATM 12 N N1 QBT . . . F 5 -15.807 -19.121 -13.239 1 48.16 ? N1 QBT 1388 A 1 HETATM 13 C C2 QBT . . . F 5 -16.47 -19.235 -14.467 1 55.56 ? C2 QBT 1388 A 1 HETATM 14 O O2 QBT . . . F 5 -16.264 -18.394 -15.36 1 48.29 ? O2 QBT 1388 A 1 HETATM 15 N N3 QBT . . . F 5 -17.249 -20.254 -14.749 1 45.8 ? N3 QBT 1388 A 1 HETATM 16 C C4 QBT . . . F 5 -17.524 -21.17 -13.845 1 50.97 ? C4 QBT 1388 A 1 HETATM 17 O O4 QBT . . . F 5 -18.271 -22.134 -14.075 1 44.81 ? O4 QBT 1388 A 1 HETATM 18 C C5 QBT . . . F 5 -16.823 -21.096 -12.555 1 43.84 ? C5 QBT 1388 A 1 HETATM 19 C C6 QBT . . . F 5 -16 -20.024 -12.326 1 45.42 ? C6 QBT 1388 A 1 HETATM 20 C C5M QBT . . . F 5 -17.082 -22.17 -11.551 1 43.13 ? C5M QBT 1388 A 1 HETATM 21 O O3P QBT . . . F 5 -9.733 -18.294 -9.388 0.5 58.92 ? O3P QBT 1388 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #