data_1H7L # _model_server_result.job_id hfdFkbQFvgo_xXCI-lIXzA _model_server_result.datetime_utc '2024-12-21 15:35:26' _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 1h7l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1258}' # _entry.id 1H7L # _exptl.entry_id 1H7L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _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 1H7L _cell.length_a 47.32 _cell.length_b 142.31 _cell.length_c 81.31 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1H7L _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _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 3 _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 154 A CYS 155 1_555 A SG CYS 242 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc1 A OD2 ASP 98 A ASP 99 1_555 B MG MG . A MG 1257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc2 B MG MG . A MG 1257 1_555 C O2A TYD . A TYD 1258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc3 B MG MG . A MG 1257 1_555 C O3B TYD . A TYD 1258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? metalc ? metalc4 C O1B TYD . A TYD 1258 1_555 D MG MG . A MG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.086 ? metalc ? metalc5 D MG MG . A MG 1259 1_555 E O HOH . A HOH 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.138 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A TYD doub 334 n n PA O2A TYD sing 335 n n PA O3A TYD sing 336 n n PA O5' TYD sing 337 n n O2A HOA2 TYD sing 338 n n O3A PB TYD sing 339 n n PB O1B TYD doub 340 n n PB O2B TYD sing 341 n n PB O3B TYD sing 342 n n O2B HOB2 TYD sing 343 n n O3B HOB3 TYD sing 344 n n O5' C5' TYD sing 345 n n C5' C4' TYD sing 346 n n C5' "H5'1" TYD sing 347 n n C5' "H5'2" TYD sing 348 n n C4' O4' TYD sing 349 n n C4' C3' TYD sing 350 n n C4' H4' TYD sing 351 n n O4' C1' TYD sing 352 n n C3' O3' TYD sing 353 n n C3' C2' TYD sing 354 n n C3' H3' TYD sing 355 n n O3' HO3' TYD sing 356 n n C2' C1' TYD sing 357 n n C2' "H2'1" TYD sing 358 n n C2' "H2'2" TYD sing 359 n n C1' N1 TYD sing 360 n n C1' H1' TYD sing 361 n n N1 C2 TYD sing 362 n y N1 C6 TYD sing 363 n y C2 O2 TYD doub 364 n n C2 N3 TYD sing 365 n y N3 C4 TYD sing 366 n y N3 HN3 TYD sing 367 n n C4 O4 TYD doub 368 n n C4 C5 TYD sing 369 n y C5 C5M TYD sing 370 n n C5 C6 TYD doub 371 n y C5M H51 TYD sing 372 n n C5M H52 TYD sing 373 n n C5M H53 TYD sing 374 n n C6 H6 TYD sing 375 n n # _atom_sites.entry_id 1H7L _atom_sites.fract_transf_matrix[1][1] 0.021133 _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] 0.007027 _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] 0.012299 _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 MG A 1 1257 1257 MG MG . C 3 TYD A 1 1258 1258 TYD TYD . D 2 MG A 1 1259 1259 MG MG . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 HOH HOH . E 4 HOH A 51 2051 2051 HOH HOH . E 4 HOH A 52 2052 2052 HOH HOH . E 4 HOH A 53 2053 2053 HOH HOH . E 4 HOH A 54 2054 2054 HOH HOH . E 4 HOH A 55 2055 2055 HOH HOH . E 4 HOH A 56 2056 2056 HOH HOH . E 4 HOH A 57 2057 2057 HOH HOH . E 4 HOH A 58 2058 2058 HOH HOH . E 4 HOH A 59 2059 2059 HOH HOH . E 4 HOH A 60 2060 2060 HOH HOH . E 4 HOH A 61 2061 2061 HOH HOH . E 4 HOH A 62 2062 2062 HOH HOH . E 4 HOH A 63 2063 2063 HOH HOH . E 4 HOH A 64 2064 2064 HOH HOH . E 4 HOH A 65 2065 2065 HOH HOH . E 4 HOH A 66 2066 2066 HOH HOH . E 4 HOH A 67 2067 2067 HOH HOH . E 4 HOH A 68 2068 2068 HOH HOH . E 4 HOH A 69 2069 2069 HOH HOH . E 4 HOH A 70 2070 2070 HOH HOH . E 4 HOH A 71 2071 2071 HOH HOH . E 4 HOH A 72 2072 2072 HOH HOH . E 4 HOH A 73 2073 2073 HOH HOH . E 4 HOH A 74 2074 2074 HOH HOH . E 4 HOH A 75 2075 2075 HOH HOH . E 4 HOH A 76 2076 2076 HOH HOH . E 4 HOH A 77 2077 2077 HOH HOH . E 4 HOH A 78 2078 2078 HOH HOH . E 4 HOH A 79 2079 2079 HOH HOH . E 4 HOH A 80 2080 2080 HOH HOH . E 4 HOH A 81 2081 2081 HOH HOH . E 4 HOH A 82 2082 2082 HOH HOH . E 4 HOH A 83 2083 2083 HOH HOH . E 4 HOH A 84 2084 2084 HOH HOH . E 4 HOH A 85 2085 2085 HOH HOH . E 4 HOH A 86 2086 2086 HOH HOH . E 4 HOH A 87 2087 2087 HOH HOH . E 4 HOH A 88 2088 2088 HOH HOH . E 4 HOH A 89 2089 2089 HOH HOH . E 4 HOH A 90 2090 2090 HOH HOH . E 4 HOH A 91 2091 2091 HOH HOH . E 4 HOH A 92 2092 2092 HOH HOH . E 4 HOH A 93 2093 2093 HOH HOH . E 4 HOH A 94 2094 2094 HOH HOH . E 4 HOH A 95 2095 2095 HOH HOH . E 4 HOH A 96 2096 2096 HOH HOH . E 4 HOH A 97 2097 2097 HOH HOH . E 4 HOH A 98 2098 2098 HOH HOH . E 4 HOH A 99 2099 2099 HOH HOH . E 4 HOH A 100 2100 2100 HOH HOH . E 4 HOH A 101 2101 2101 HOH HOH . E 4 HOH A 102 2102 2102 HOH HOH . E 4 HOH A 103 2103 2103 HOH HOH . E 4 HOH A 104 2104 2104 HOH HOH . E 4 HOH A 105 2105 2105 HOH HOH . E 4 HOH A 106 2106 2106 HOH HOH . E 4 HOH A 107 2107 2107 HOH HOH . E 4 HOH A 108 2108 2108 HOH HOH . E 4 HOH A 109 2109 2109 HOH HOH . E 4 HOH A 110 2110 2110 HOH HOH . E 4 HOH A 111 2111 2111 HOH HOH . E 4 HOH A 112 2112 2112 HOH HOH . E 4 HOH A 113 2113 2113 HOH HOH . E 4 HOH A 114 2114 2114 HOH HOH . E 4 HOH A 115 2115 2115 HOH HOH . E 4 HOH A 116 2116 2116 HOH HOH . E 4 HOH A 117 2117 2117 HOH HOH . E 4 HOH A 118 2118 2118 HOH HOH . E 4 HOH A 119 2119 2119 HOH HOH . E 4 HOH A 120 2120 2120 HOH HOH . E 4 HOH A 121 2121 2121 HOH HOH . E 4 HOH A 122 2122 2122 HOH HOH . E 4 HOH A 123 2123 2123 HOH HOH . E 4 HOH A 124 2124 2124 HOH HOH . E 4 HOH A 125 2125 2125 HOH HOH . E 4 HOH A 126 2126 2126 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 PA TYD . . . C 3 16.872 14.528 34.753 1 45.15 ? PA TYD 1258 A 1 HETATM 2 O O1A TYD . . . C 3 18.15 14.063 34.105 1 43.85 ? O1A TYD 1258 A 1 HETATM 3 O O2A TYD . . . C 3 15.575 14.218 34.065 1 43.27 ? O2A TYD 1258 A 1 HETATM 4 O O3A TYD . . . C 3 16.75 14.003 36.265 1 49.98 ? O3A TYD 1258 A 1 HETATM 5 P PB TYD . . . C 3 16.176 12.529 36.611 1 54.49 ? PB TYD 1258 A 1 HETATM 6 O O1B TYD . . . C 3 15.405 12.679 37.902 1 55.13 ? O1B TYD 1258 A 1 HETATM 7 O O2B TYD . . . C 3 17.494 11.821 36.712 1 53.97 ? O2B TYD 1258 A 1 HETATM 8 O O3B TYD . . . C 3 15.325 12.065 35.466 1 54.67 ? O3B TYD 1258 A 1 HETATM 9 O O5' TYD . . . C 3 17.048 16.109 35.021 1 38.12 ? O5' TYD 1258 A 1 HETATM 10 C C5' TYD . . . C 3 16.12 16.892 35.767 1 33.67 ? C5' TYD 1258 A 1 HETATM 11 C C4' TYD . . . C 3 15.91 18.193 35 1 31.45 ? C4' TYD 1258 A 1 HETATM 12 O O4' TYD . . . C 3 17.145 18.906 34.915 1 27.65 ? O4' TYD 1258 A 1 HETATM 13 C C3' TYD . . . C 3 15.458 17.921 33.58 1 28.48 ? C3' TYD 1258 A 1 HETATM 14 O O3' TYD . . . C 3 14.263 18.652 33.377 1 29.05 ? O3' TYD 1258 A 1 HETATM 15 C C2' TYD . . . C 3 16.595 18.42 32.721 1 29.49 ? C2' TYD 1258 A 1 HETATM 16 C C1' TYD . . . C 3 17.255 19.464 33.628 1 27.28 ? C1' TYD 1258 A 1 HETATM 17 N N1 TYD . . . C 3 18.667 19.702 33.391 1 26.47 ? N1 TYD 1258 A 1 HETATM 18 C C2 TYD . . . C 3 19.11 20.934 33.11 1 27.3 ? C2 TYD 1258 A 1 HETATM 19 O O2 TYD . . . C 3 18.276 21.87 33.062 1 25.36 ? O2 TYD 1258 A 1 HETATM 20 N N3 TYD . . . C 3 20.418 21.185 32.885 1 27.48 ? N3 TYD 1258 A 1 HETATM 21 C C4 TYD . . . C 3 21.36 20.213 32.926 1 28.38 ? C4 TYD 1258 A 1 HETATM 22 O O4 TYD . . . C 3 22.586 20.437 32.702 1 26.19 ? O4 TYD 1258 A 1 HETATM 23 C C5 TYD . . . C 3 20.883 18.855 33.256 1 28.09 ? C5 TYD 1258 A 1 HETATM 24 C C5M TYD . . . C 3 21.851 17.688 33.326 1 28.68 ? C5M TYD 1258 A 1 HETATM 25 C C6 TYD . . . C 3 19.521 18.674 33.466 1 28.6 ? C6 TYD 1258 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #