data_1Z4Q # _model_server_result.job_id 5TGGHc9oaXvn0S2kLfzfzA _model_server_result.datetime_utc '2024-10-12 21:22:21' _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 1z4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1489}' # _entry.id 1Z4Q # _exptl.entry_id 1Z4Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 304.193 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-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 1Z4Q _cell.length_a 73.77 _cell.length_b 73.77 _cell.length_c 106.057 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z4Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 1,2 # 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 73.77 73.77 53.0285 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 metalc ? metalc1 A OD1 ASN 10 A ASN 41 1_555 C MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc2 A O ASP 12 A ASP 43 1_555 C MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc3 A O ALA 88 A ALA 119 1_555 B MG MG . A MG 2229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc4 A O LEU 90 A LEU 121 1_555 B MG MG . A MG 2229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc5 A O THR 93 A THR 124 1_555 B MG MG . A MG 2229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc6 A OD1 ASP 145 A ASP 176 1_555 C MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc7 D OP3 D4M . A D4M 1489 1_555 C MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc8 C MG MG . A MG 2001 1_555 E O HOH . A HOH 2264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc9 C MG MG . A MG 2001 1_555 E O HOH . A HOH 2309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc10 B MG MG . A MG 2229 1_555 E O HOH . A HOH 2330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc11 B MG MG . A MG 2229 1_555 E O HOH . A HOH 2349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc12 B MG MG . A MG 2229 1_555 E O HOH . A HOH 2376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? # _chem_comp.formula 'C10 H13 N2 O7 P' _chem_comp.formula_weight 304.193 _chem_comp.id D4M _chem_comp.mon_nstd_flag n _chem_comp.name '[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE' _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "2',3'-DIDEOXY-2',3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE;2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-MONOPHOSPHATE" # 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 OP2 P D4M sing 83 n n OP2 HOP2 D4M sing 84 n n P OP1 D4M doub 85 n n P OP3 D4M sing 86 n n P O5' D4M sing 87 n n OP3 HOP3 D4M sing 88 n n O5' C5' D4M sing 89 n n C5' C4' D4M sing 90 n n C5' H5' D4M sing 91 n n C5' "H5''" D4M sing 92 n n C4' O4' D4M sing 93 n n C4' C3' D4M sing 94 n n C4' H4' D4M sing 95 n n O4' C1' D4M sing 96 n n C3' C2' D4M doub 97 n n C3' H3' D4M sing 98 n n C2' C1' D4M sing 99 n n C2' H2' D4M sing 100 n n C1' N1 D4M sing 101 n n C1' H1' D4M sing 102 n n N1 C6 D4M sing 103 n n N1 C2 D4M sing 104 n n C6 C5 D4M doub 105 n n C6 H6 D4M sing 106 n n C5 C5M D4M sing 107 n n C5 C4 D4M sing 108 n n C5M H71 D4M sing 109 n n C5M H72 D4M sing 110 n n C5M H73 D4M sing 111 n n C4 O4 D4M doub 112 n n C4 N3 D4M sing 113 n n N3 C2 D4M sing 114 n n N3 H3 D4M sing 115 n n C2 O2 D4M doub 116 n n # _atom_sites.entry_id 1Z4Q _atom_sites.fract_transf_matrix[1][1] 0.013556 _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] 0.013556 _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] 0.009429 _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 2229 2229 MG MG . C 2 MG A 1 2001 2001 MG MG . D 3 D4M A 1 1489 1489 D4M D4M . E 4 HOH A 1 2230 1 HOH HOH . E 4 HOH A 2 2231 2 HOH HOH . E 4 HOH A 3 2232 3 HOH HOH . E 4 HOH A 4 2233 4 HOH HOH . E 4 HOH A 5 2234 5 HOH HOH . E 4 HOH A 6 2235 6 HOH HOH . E 4 HOH A 7 2236 8 HOH HOH . E 4 HOH A 8 2237 9 HOH HOH . E 4 HOH A 9 2238 10 HOH HOH . E 4 HOH A 10 2239 11 HOH HOH . E 4 HOH A 11 2240 12 HOH HOH . E 4 HOH A 12 2241 13 HOH HOH . E 4 HOH A 13 2242 14 HOH HOH . E 4 HOH A 14 2243 15 HOH HOH . E 4 HOH A 15 2244 16 HOH HOH . E 4 HOH A 16 2245 17 HOH HOH . E 4 HOH A 17 2246 18 HOH HOH . E 4 HOH A 18 2247 19 HOH HOH . E 4 HOH A 19 2248 20 HOH HOH . E 4 HOH A 20 2249 21 HOH HOH . E 4 HOH A 21 2250 22 HOH HOH . E 4 HOH A 22 2251 23 HOH HOH . E 4 HOH A 23 2252 24 HOH HOH . E 4 HOH A 24 2253 25 HOH HOH . E 4 HOH A 25 2254 26 HOH HOH . E 4 HOH A 26 2255 28 HOH HOH . E 4 HOH A 27 2256 29 HOH HOH . E 4 HOH A 28 2257 30 HOH HOH . E 4 HOH A 29 2258 31 HOH HOH . E 4 HOH A 30 2259 32 HOH HOH . E 4 HOH A 31 2260 33 HOH HOH . E 4 HOH A 32 2261 34 HOH HOH . E 4 HOH A 33 2262 35 HOH HOH . E 4 HOH A 34 2263 36 HOH HOH . E 4 HOH A 35 2264 37 HOH HOH . E 4 HOH A 36 2265 38 HOH HOH . E 4 HOH A 37 2266 39 HOH HOH . E 4 HOH A 38 2267 40 HOH HOH . E 4 HOH A 39 2268 41 HOH HOH . E 4 HOH A 40 2269 43 HOH HOH . E 4 HOH A 41 2270 44 HOH HOH . E 4 HOH A 42 2271 48 HOH HOH . E 4 HOH A 43 2272 49 HOH HOH . E 4 HOH A 44 2273 50 HOH HOH . E 4 HOH A 45 2274 51 HOH HOH . E 4 HOH A 46 2275 52 HOH HOH . E 4 HOH A 47 2276 53 HOH HOH . E 4 HOH A 48 2277 54 HOH HOH . E 4 HOH A 49 2278 55 HOH HOH . E 4 HOH A 50 2279 56 HOH HOH . E 4 HOH A 51 2280 57 HOH HOH . E 4 HOH A 52 2281 58 HOH HOH . E 4 HOH A 53 2282 59 HOH HOH . E 4 HOH A 54 2283 60 HOH HOH . E 4 HOH A 55 2284 61 HOH HOH . E 4 HOH A 56 2285 62 HOH HOH . E 4 HOH A 57 2286 63 HOH HOH . E 4 HOH A 58 2287 64 HOH HOH . E 4 HOH A 59 2288 65 HOH HOH . E 4 HOH A 60 2289 66 HOH HOH . E 4 HOH A 61 2290 67 HOH HOH . E 4 HOH A 62 2291 68 HOH HOH . E 4 HOH A 63 2292 69 HOH HOH . E 4 HOH A 64 2293 70 HOH HOH . E 4 HOH A 65 2294 71 HOH HOH . E 4 HOH A 66 2295 72 HOH HOH . E 4 HOH A 67 2296 73 HOH HOH . E 4 HOH A 68 2297 74 HOH HOH . E 4 HOH A 69 2298 75 HOH HOH . E 4 HOH A 70 2299 76 HOH HOH . E 4 HOH A 71 2300 77 HOH HOH . E 4 HOH A 72 2301 78 HOH HOH . E 4 HOH A 73 2302 79 HOH HOH . E 4 HOH A 74 2303 80 HOH HOH . E 4 HOH A 75 2304 81 HOH HOH . E 4 HOH A 76 2305 82 HOH HOH . E 4 HOH A 77 2306 83 HOH HOH . E 4 HOH A 78 2307 86 HOH HOH . E 4 HOH A 79 2308 87 HOH HOH . E 4 HOH A 80 2309 88 HOH HOH . E 4 HOH A 81 2310 89 HOH HOH . E 4 HOH A 82 2311 90 HOH HOH . E 4 HOH A 83 2312 91 HOH HOH . E 4 HOH A 84 2313 92 HOH HOH . E 4 HOH A 85 2314 93 HOH HOH . E 4 HOH A 86 2315 94 HOH HOH . E 4 HOH A 87 2316 95 HOH HOH . E 4 HOH A 88 2317 96 HOH HOH . E 4 HOH A 89 2318 97 HOH HOH . E 4 HOH A 90 2319 98 HOH HOH . E 4 HOH A 91 2320 99 HOH HOH . E 4 HOH A 92 2321 100 HOH HOH . E 4 HOH A 93 2322 101 HOH HOH . E 4 HOH A 94 2323 102 HOH HOH . E 4 HOH A 95 2324 103 HOH HOH . E 4 HOH A 96 2325 104 HOH HOH . E 4 HOH A 97 2326 105 HOH HOH . E 4 HOH A 98 2327 106 HOH HOH . E 4 HOH A 99 2328 107 HOH HOH . E 4 HOH A 100 2329 108 HOH HOH . E 4 HOH A 101 2330 109 HOH HOH . E 4 HOH A 102 2331 110 HOH HOH . E 4 HOH A 103 2332 111 HOH HOH . E 4 HOH A 104 2333 112 HOH HOH . E 4 HOH A 105 2334 113 HOH HOH . E 4 HOH A 106 2335 114 HOH HOH . E 4 HOH A 107 2336 115 HOH HOH . E 4 HOH A 108 2337 116 HOH HOH . E 4 HOH A 109 2338 117 HOH HOH . E 4 HOH A 110 2339 118 HOH HOH . E 4 HOH A 111 2340 119 HOH HOH . E 4 HOH A 112 2341 120 HOH HOH . E 4 HOH A 113 2342 121 HOH HOH . E 4 HOH A 114 2343 122 HOH HOH . E 4 HOH A 115 2344 123 HOH HOH . E 4 HOH A 116 2345 124 HOH HOH . E 4 HOH A 117 2346 125 HOH HOH . E 4 HOH A 118 2347 126 HOH HOH . E 4 HOH A 119 2348 127 HOH HOH . E 4 HOH A 120 2349 128 HOH HOH . E 4 HOH A 121 2350 129 HOH HOH . E 4 HOH A 122 2351 130 HOH HOH . E 4 HOH A 123 2352 131 HOH HOH . E 4 HOH A 124 2353 132 HOH HOH . E 4 HOH A 125 2354 133 HOH HOH . E 4 HOH A 126 2355 134 HOH HOH . E 4 HOH A 127 2356 136 HOH HOH . E 4 HOH A 128 2357 137 HOH HOH . E 4 HOH A 129 2358 138 HOH HOH . E 4 HOH A 130 2359 139 HOH HOH . E 4 HOH A 131 2360 140 HOH HOH . E 4 HOH A 132 2361 141 HOH HOH . E 4 HOH A 133 2362 142 HOH HOH . E 4 HOH A 134 2363 143 HOH HOH . E 4 HOH A 135 2364 144 HOH HOH . E 4 HOH A 136 2365 145 HOH HOH . E 4 HOH A 137 2366 146 HOH HOH . E 4 HOH A 138 2367 147 HOH HOH . E 4 HOH A 139 2368 148 HOH HOH . E 4 HOH A 140 2369 149 HOH HOH . E 4 HOH A 141 2370 150 HOH HOH . E 4 HOH A 142 2371 151 HOH HOH . E 4 HOH A 143 2372 152 HOH HOH . E 4 HOH A 144 2373 153 HOH HOH . E 4 HOH A 145 2374 154 HOH HOH . E 4 HOH A 146 2375 155 HOH HOH . E 4 HOH A 147 2376 156 HOH HOH . E 4 HOH A 148 2377 157 HOH HOH . E 4 HOH A 149 2378 158 HOH HOH . E 4 HOH A 150 2379 159 HOH HOH . E 4 HOH A 151 2380 160 HOH HOH . E 4 HOH A 152 2381 161 HOH HOH . E 4 HOH A 153 2382 162 HOH HOH . E 4 HOH A 154 2383 163 HOH HOH . E 4 HOH A 155 2384 164 HOH HOH . E 4 HOH A 156 2385 165 HOH HOH . E 4 HOH A 157 2386 166 HOH HOH . E 4 HOH A 158 2387 167 HOH HOH . E 4 HOH A 159 2388 168 HOH HOH . E 4 HOH A 160 2389 169 HOH HOH . E 4 HOH A 161 2390 170 HOH HOH . E 4 HOH A 162 2391 171 HOH HOH . E 4 HOH A 163 2392 172 HOH HOH . E 4 HOH A 164 2393 173 HOH HOH . E 4 HOH A 165 2394 174 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 OP2 D4M . . . D 3 17.153 38.848 28.332 1 19.13 ? OP2 D4M 1489 A 1 HETATM 2 P P D4M . . . D 3 16.496 40.073 29.009 1 29.63 ? P D4M 1489 A 1 HETATM 3 O OP1 D4M . . . D 3 17.643 41.181 29.184 1 21.74 ? OP1 D4M 1489 A 1 HETATM 4 O OP3 D4M . . . D 3 15.868 39.871 30.4 1 24.41 ? OP3 D4M 1489 A 1 HETATM 5 O O5' D4M . . . D 3 15.37 40.574 27.944 1 29.52 ? O5' D4M 1489 A 1 HETATM 6 C C5' D4M . . . D 3 14.189 41.27 28.442 1 29.49 ? C5' D4M 1489 A 1 HETATM 7 C C4' D4M . . . D 3 13.921 42.352 27.407 1 33.72 ? C4' D4M 1489 A 1 HETATM 8 O O4' D4M . . . D 3 13.48 41.639 26.176 1 33.16 ? O4' D4M 1489 A 1 HETATM 9 C C3' D4M . . . D 3 12.783 43.259 27.861 1 30.75 ? C3' D4M 1489 A 1 HETATM 10 C C2' D4M . . . D 3 11.829 43.224 26.934 1 31.07 ? C2' D4M 1489 A 1 HETATM 11 C C1' D4M . . . D 3 12.207 42.268 25.783 1 31.54 ? C1' D4M 1489 A 1 HETATM 12 N N1 D4M . . . D 3 11.163 41.234 25.544 1 33.11 ? N1 D4M 1489 A 1 HETATM 13 C C6 D4M . . . D 3 10.703 40.403 26.598 1 27.52 ? C6 D4M 1489 A 1 HETATM 14 C C5 D4M . . . D 3 9.728 39.435 26.36 1 30.09 ? C5 D4M 1489 A 1 HETATM 15 C C5M D4M . . . D 3 9.305 38.526 27.522 1 23.94 ? C5M D4M 1489 A 1 HETATM 16 C C4 D4M . . . D 3 9.164 39.281 25.07 1 31.73 ? C4 D4M 1489 A 1 HETATM 17 O O4 D4M . . . D 3 8.302 38.43 24.755 1 30.72 ? O4 D4M 1489 A 1 HETATM 18 N N3 D4M . . . D 3 9.602 40.108 24.066 1 29.81 ? N3 D4M 1489 A 1 HETATM 19 C C2 D4M . . . D 3 10.582 41.062 24.249 1 33.66 ? C2 D4M 1489 A 1 HETATM 20 O O2 D4M . . . D 3 10.893 41.742 23.269 1 35.52 ? O2 D4M 1489 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #