data_5FUV # _model_server_result.job_id 7V3nmorlG2QTg5q4pUTHaQ _model_server_result.datetime_utc '2024-11-23 07:28:01' _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 5fuv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1388}' # _entry.id 5FUV # _exptl.entry_id 5FUV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _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 5FUV _cell.length_a 114.68 _cell.length_b 114.68 _cell.length_c 105.6 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FUV _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,L _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 ? 4 F N N ? 4 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc1 A SG CYS 139 A CYS 341 1_555 G ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc2 A SG CYS 142 A CYS 344 1_555 G ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 A SG CYS 172 A CYS 374 1_555 G ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc4 A SG CYS 175 A CYS 377 1_555 G ZN ZN . A ZN 1389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc5 B SG CYS 139 B CYS 341 1_555 J ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc6 B SG CYS 142 B CYS 344 1_555 J ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc7 B SG CYS 172 B CYS 374 1_555 J ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc8 B SG CYS 175 B CYS 377 1_555 J ZN ZN . B ZN 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # 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 O5' C5' THM sing 307 n n O5' HO5' THM sing 308 n n C5' C4' THM sing 309 n n C5' "H5'1" THM sing 310 n n C5' "H5'2" THM sing 311 n n C4' O4' THM sing 312 n n C4' C3' THM sing 313 n n C4' H4' THM sing 314 n n O4' C1' THM sing 315 n n C3' O3' THM sing 316 n n C3' C2' THM sing 317 n n C3' H3' THM sing 318 n n O3' HO3' THM sing 319 n n C2' C1' THM sing 320 n n C2' "H2'1" THM sing 321 n n C2' "H2'2" THM sing 322 n n C1' N1 THM sing 323 n n C1' H1' THM sing 324 n n N1 C2 THM sing 325 n n N1 C6 THM sing 326 n n C2 O2 THM doub 327 n n C2 N3 THM sing 328 n n N3 C4 THM sing 329 n n N3 HN3 THM sing 330 n n C4 O4 THM doub 331 n n C4 C5 THM sing 332 n n C5 C5M THM sing 333 n n C5 C6 THM doub 334 n n C5M HM51 THM sing 335 n n C5M HM52 THM sing 336 n n C5M HM53 THM sing 337 n n C6 H6 THM sing 338 n n # _atom_sites.entry_id 5FUV _atom_sites.fract_transf_matrix[1][1] 0.00872 _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] 0.00872 _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] 0.00947 _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 GOL A 1 1385 1385 GOL GOL . D 2 GOL A 1 1386 1386 GOL GOL . E 3 PO4 A 1 1387 1387 PO4 PO4 . F 4 THM A 1 1388 1388 THM THM . G 5 ZN A 1 1389 1389 ZN ZN . H 2 GOL B 1 1384 1384 GOL GOL . I 4 THM B 1 1385 1385 THM THM . J 5 ZN B 1 1386 1386 ZN ZN . K 6 HOH A 1 2001 2001 HOH HOH . K 6 HOH A 2 2002 2002 HOH HOH . K 6 HOH A 3 2003 2003 HOH HOH . K 6 HOH A 4 2004 2004 HOH HOH . K 6 HOH A 5 2005 2005 HOH HOH . K 6 HOH A 6 2006 2006 HOH HOH . K 6 HOH A 7 2007 2007 HOH HOH . K 6 HOH A 8 2008 2008 HOH HOH . K 6 HOH A 9 2009 2009 HOH HOH . K 6 HOH A 10 2010 2010 HOH HOH . K 6 HOH A 11 2011 2011 HOH HOH . K 6 HOH A 12 2012 2012 HOH HOH . K 6 HOH A 13 2013 2013 HOH HOH . K 6 HOH A 14 2014 2014 HOH HOH . K 6 HOH A 15 2015 2015 HOH HOH . K 6 HOH A 16 2016 2016 HOH HOH . K 6 HOH A 17 2017 2017 HOH HOH . K 6 HOH A 18 2018 2018 HOH HOH . K 6 HOH A 19 2019 2019 HOH HOH . K 6 HOH A 20 2020 2020 HOH HOH . K 6 HOH A 21 2021 2021 HOH HOH . K 6 HOH A 22 2022 2022 HOH HOH . K 6 HOH A 23 2023 2023 HOH HOH . K 6 HOH A 24 2024 2024 HOH HOH . K 6 HOH A 25 2025 2025 HOH HOH . K 6 HOH A 26 2026 2026 HOH HOH . K 6 HOH A 27 2027 2027 HOH HOH . K 6 HOH A 28 2028 2028 HOH HOH . K 6 HOH A 29 2029 2029 HOH HOH . K 6 HOH A 30 2030 2030 HOH HOH . K 6 HOH A 31 2031 2031 HOH HOH . K 6 HOH A 32 2032 2032 HOH HOH . K 6 HOH A 33 2033 2033 HOH HOH . K 6 HOH A 34 2034 2034 HOH HOH . K 6 HOH A 35 2035 2035 HOH HOH . K 6 HOH A 36 2036 2036 HOH HOH . K 6 HOH A 37 2037 2037 HOH HOH . K 6 HOH A 38 2038 2038 HOH HOH . K 6 HOH A 39 2039 2039 HOH HOH . K 6 HOH A 40 2040 2040 HOH HOH . K 6 HOH A 41 2041 2041 HOH HOH . K 6 HOH A 42 2042 2042 HOH HOH . K 6 HOH A 43 2043 2043 HOH HOH . K 6 HOH A 44 2044 2044 HOH HOH . K 6 HOH A 45 2045 2045 HOH HOH . K 6 HOH A 46 2046 2046 HOH HOH . K 6 HOH A 47 2047 2047 HOH HOH . K 6 HOH A 48 2048 2048 HOH HOH . K 6 HOH A 49 2049 2049 HOH HOH . K 6 HOH A 50 2050 2050 HOH HOH . K 6 HOH A 51 2051 2051 HOH HOH . K 6 HOH A 52 2052 2052 HOH HOH . K 6 HOH A 53 2053 2053 HOH HOH . K 6 HOH A 54 2054 2054 HOH HOH . K 6 HOH A 55 2055 2055 HOH HOH . K 6 HOH A 56 2056 2056 HOH HOH . K 6 HOH A 57 2057 2057 HOH HOH . K 6 HOH A 58 2058 2058 HOH HOH . K 6 HOH A 59 2059 2059 HOH HOH . K 6 HOH A 60 2060 2060 HOH HOH . K 6 HOH A 61 2061 2061 HOH HOH . K 6 HOH A 62 2062 2062 HOH HOH . L 6 HOH B 1 2001 2001 HOH HOH . L 6 HOH B 2 2002 2002 HOH HOH . L 6 HOH B 3 2003 2003 HOH HOH . L 6 HOH B 4 2004 2004 HOH HOH . L 6 HOH B 5 2005 2005 HOH HOH . L 6 HOH B 6 2006 2006 HOH HOH . L 6 HOH B 7 2007 2007 HOH HOH . L 6 HOH B 8 2008 2008 HOH HOH . L 6 HOH B 9 2009 2009 HOH HOH . L 6 HOH B 10 2010 2010 HOH HOH . L 6 HOH B 11 2011 2011 HOH HOH . L 6 HOH B 12 2012 2012 HOH HOH . L 6 HOH B 13 2013 2013 HOH HOH . L 6 HOH B 14 2014 2014 HOH HOH . L 6 HOH B 15 2015 2015 HOH HOH . L 6 HOH B 16 2016 2016 HOH HOH . L 6 HOH B 17 2017 2017 HOH HOH . L 6 HOH B 18 2018 2018 HOH HOH . L 6 HOH B 19 2019 2019 HOH HOH . L 6 HOH B 20 2020 2020 HOH HOH . L 6 HOH B 21 2021 2021 HOH HOH . L 6 HOH B 22 2022 2022 HOH HOH . L 6 HOH B 23 2023 2023 HOH HOH . L 6 HOH B 24 2024 2024 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 O O5' THM . . . F 4 -11.597 -17.933 -10.269 1 51.02 ? O5' THM 1388 A 1 HETATM 2 C C5' THM . . . F 4 -12.563 -18.58 -11.042 1 48.06 ? C5' THM 1388 A 1 HETATM 3 C C4' THM . . . F 4 -13.025 -17.617 -12.104 1 42.53 ? C4' THM 1388 A 1 HETATM 4 O O4' THM . . . F 4 -13.805 -18.479 -12.919 1 43.94 ? O4' THM 1388 A 1 HETATM 5 C C3' THM . . . F 4 -13.908 -16.545 -11.501 1 41.43 ? C3' THM 1388 A 1 HETATM 6 O O3' THM . . . F 4 -13.753 -15.328 -12.205 1 43.22 ? O3' THM 1388 A 1 HETATM 7 C C2' THM . . . F 4 -15.33 -17.05 -11.667 1 44.01 ? C2' THM 1388 A 1 HETATM 8 C C1' THM . . . F 4 -15.114 -17.891 -12.901 1 44.86 ? C1' THM 1388 A 1 HETATM 9 N N1 THM . . . F 4 -15.968 -19.032 -13.065 1 45.39 ? N1 THM 1388 A 1 HETATM 10 C C2 THM . . . F 4 -16.578 -19.203 -14.338 1 46.47 ? C2 THM 1388 A 1 HETATM 11 O O2 THM . . . F 4 -16.413 -18.346 -15.254 1 46.79 ? O2 THM 1388 A 1 HETATM 12 N N3 THM . . . F 4 -17.34 -20.262 -14.577 1 40.16 ? N3 THM 1388 A 1 HETATM 13 C C4 THM . . . F 4 -17.606 -21.171 -13.662 1 48.21 ? C4 THM 1388 A 1 HETATM 14 O O4 THM . . . F 4 -18.307 -22.167 -13.935 1 43.24 ? O4 THM 1388 A 1 HETATM 15 C C5 THM . . . F 4 -16.913 -21.054 -12.336 1 44.91 ? C5 THM 1388 A 1 HETATM 16 C C5M THM . . . F 4 -17.126 -22.093 -11.278 1 46.72 ? C5M THM 1388 A 1 HETATM 17 C C6 THM . . . F 4 -16.138 -19.941 -12.115 1 45.76 ? C6 THM 1388 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 17 #