data_3G1D # _model_server_result.job_id e6l99raZEU3ZgrjxZWdbFw _model_server_result.datetime_utc '2024-10-17 01:47:06' _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 3g1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":229}' # _entry.id 3G1D # _exptl.entry_id 3G1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 115.41 _cell.angle_gamma 90 _cell.entry_id 3G1D _cell.length_a 59.569 _cell.length_b 64.224 _cell.length_c 61.823 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3G1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 330 n n N1 C6 U5P sing 331 n n N1 C1' U5P sing 332 n n C2 N3 U5P sing 333 n n C2 O2 U5P doub 334 n n N3 C4 U5P sing 335 n n N3 HN3 U5P sing 336 n n C4 C5 U5P sing 337 n n C4 O4 U5P doub 338 n n C5 C6 U5P doub 339 n n C5 H5 U5P sing 340 n n C6 H6 U5P sing 341 n n C1' C2' U5P sing 342 n n C1' O4' U5P sing 343 n n C1' H1' U5P sing 344 n n C2' O2' U5P sing 345 n n C2' C3' U5P sing 346 n n C2' H2' U5P sing 347 n n O2' HO2' U5P sing 348 n n C3' C4' U5P sing 349 n n C3' O3' U5P sing 350 n n C3' H3' U5P sing 351 n n C4' O4' U5P sing 352 n n C4' C5' U5P sing 353 n n C4' H4' U5P sing 354 n n O3' HO3' U5P sing 355 n n C5' O5' U5P sing 356 n n C5' "H5'1" U5P sing 357 n n C5' "H5'2" U5P sing 358 n n O5' P U5P sing 359 n n P O1P U5P doub 360 n n P O2P U5P sing 361 n n P O3P U5P sing 362 n n O2P HOP2 U5P sing 363 n n O3P HOP3 U5P sing 364 n n # _atom_sites.entry_id 3G1D _atom_sites.fract_transf_matrix[1][1] 0.016787 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007975 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015571 _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] 0.017908 _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 U5P A 1 229 1 U5P U . D 2 U5P B 1 229 2 U5P U . E 3 HOH A 1 230 2 HOH HOH . E 3 HOH A 2 231 3 HOH HOH . E 3 HOH A 3 232 232 HOH HOH . E 3 HOH A 4 233 6 HOH HOH . E 3 HOH A 5 234 234 HOH HOH . E 3 HOH A 6 235 9 HOH HOH . E 3 HOH A 7 236 236 HOH HOH . E 3 HOH A 8 237 12 HOH HOH . E 3 HOH A 9 238 238 HOH HOH . E 3 HOH A 10 239 13 HOH HOH . E 3 HOH A 11 240 17 HOH HOH . E 3 HOH A 12 241 18 HOH HOH . E 3 HOH A 13 242 20 HOH HOH . E 3 HOH A 14 243 21 HOH HOH . E 3 HOH A 15 244 244 HOH HOH . E 3 HOH A 16 245 245 HOH HOH . E 3 HOH A 17 246 25 HOH HOH . E 3 HOH A 18 247 27 HOH HOH . E 3 HOH A 19 248 29 HOH HOH . E 3 HOH A 20 249 30 HOH HOH . E 3 HOH A 21 250 250 HOH HOH . E 3 HOH A 22 251 31 HOH HOH . E 3 HOH A 23 252 32 HOH HOH . E 3 HOH A 24 253 253 HOH HOH . E 3 HOH A 25 254 41 HOH HOH . E 3 HOH A 26 255 255 HOH HOH . E 3 HOH A 27 256 256 HOH HOH . E 3 HOH A 28 257 43 HOH HOH . E 3 HOH A 29 258 44 HOH HOH . E 3 HOH A 30 259 49 HOH HOH . E 3 HOH A 31 260 260 HOH HOH . E 3 HOH A 32 261 53 HOH HOH . E 3 HOH A 33 262 60 HOH HOH . E 3 HOH A 34 263 61 HOH HOH . E 3 HOH A 35 264 62 HOH HOH . E 3 HOH A 36 266 64 HOH HOH . E 3 HOH A 37 267 66 HOH HOH . E 3 HOH A 38 268 67 HOH HOH . E 3 HOH A 39 269 69 HOH HOH . E 3 HOH A 40 270 70 HOH HOH . E 3 HOH A 41 271 271 HOH HOH . E 3 HOH A 42 272 72 HOH HOH . E 3 HOH A 43 273 76 HOH HOH . E 3 HOH A 44 274 274 HOH HOH . E 3 HOH A 45 275 275 HOH HOH . E 3 HOH A 46 276 78 HOH HOH . E 3 HOH A 47 277 79 HOH HOH . E 3 HOH A 48 278 278 HOH HOH . E 3 HOH A 49 279 82 HOH HOH . E 3 HOH A 50 280 83 HOH HOH . E 3 HOH A 51 281 86 HOH HOH . E 3 HOH A 52 282 87 HOH HOH . E 3 HOH A 53 283 88 HOH HOH . E 3 HOH A 54 284 89 HOH HOH . E 3 HOH A 55 285 95 HOH HOH . E 3 HOH A 56 286 97 HOH HOH . E 3 HOH A 57 287 98 HOH HOH . E 3 HOH A 58 288 100 HOH HOH . E 3 HOH A 59 289 101 HOH HOH . E 3 HOH A 60 290 105 HOH HOH . E 3 HOH A 61 291 106 HOH HOH . E 3 HOH A 62 292 108 HOH HOH . E 3 HOH A 63 293 109 HOH HOH . E 3 HOH A 64 294 110 HOH HOH . E 3 HOH A 65 295 111 HOH HOH . E 3 HOH A 66 296 113 HOH HOH . E 3 HOH A 67 297 114 HOH HOH . E 3 HOH A 68 298 115 HOH HOH . E 3 HOH A 69 299 116 HOH HOH . E 3 HOH A 70 300 117 HOH HOH . E 3 HOH A 71 301 126 HOH HOH . E 3 HOH A 72 302 129 HOH HOH . E 3 HOH A 73 304 132 HOH HOH . E 3 HOH A 74 305 133 HOH HOH . E 3 HOH A 75 306 134 HOH HOH . E 3 HOH A 76 307 136 HOH HOH . E 3 HOH A 77 308 137 HOH HOH . E 3 HOH A 78 309 138 HOH HOH . E 3 HOH A 79 310 139 HOH HOH . E 3 HOH A 80 311 140 HOH HOH . E 3 HOH A 81 312 141 HOH HOH . E 3 HOH A 82 313 144 HOH HOH . E 3 HOH A 83 314 145 HOH HOH . E 3 HOH A 84 315 146 HOH HOH . E 3 HOH A 85 316 147 HOH HOH . E 3 HOH A 86 317 150 HOH HOH . E 3 HOH A 87 318 153 HOH HOH . E 3 HOH A 88 319 163 HOH HOH . E 3 HOH A 89 320 165 HOH HOH . E 3 HOH A 90 321 167 HOH HOH . E 3 HOH A 91 322 171 HOH HOH . E 3 HOH A 92 323 172 HOH HOH . E 3 HOH A 93 325 176 HOH HOH . E 3 HOH A 94 326 177 HOH HOH . E 3 HOH A 95 327 178 HOH HOH . E 3 HOH A 96 328 179 HOH HOH . E 3 HOH A 97 329 180 HOH HOH . E 3 HOH A 98 330 182 HOH HOH . E 3 HOH A 99 331 184 HOH HOH . E 3 HOH A 100 332 185 HOH HOH . E 3 HOH A 101 333 187 HOH HOH . E 3 HOH A 102 334 190 HOH HOH . E 3 HOH A 103 335 193 HOH HOH . E 3 HOH A 104 336 194 HOH HOH . E 3 HOH A 105 337 196 HOH HOH . E 3 HOH A 106 338 199 HOH HOH . E 3 HOH A 107 339 200 HOH HOH . E 3 HOH A 108 340 202 HOH HOH . E 3 HOH A 109 341 203 HOH HOH . E 3 HOH A 110 342 207 HOH HOH . E 3 HOH A 111 343 209 HOH HOH . E 3 HOH A 112 344 210 HOH HOH . E 3 HOH A 113 345 213 HOH HOH . E 3 HOH A 114 347 216 HOH HOH . E 3 HOH A 115 348 218 HOH HOH . E 3 HOH A 116 349 220 HOH HOH . E 3 HOH A 117 350 221 HOH HOH . E 3 HOH A 118 351 222 HOH HOH . E 3 HOH A 119 352 223 HOH HOH . E 3 HOH A 120 353 224 HOH HOH . E 3 HOH A 121 354 225 HOH HOH . E 3 HOH A 122 355 228 HOH HOH . F 3 HOH B 1 230 5 HOH HOH . F 3 HOH B 2 231 7 HOH HOH . F 3 HOH B 3 232 8 HOH HOH . F 3 HOH B 4 233 10 HOH HOH . F 3 HOH B 5 234 11 HOH HOH . F 3 HOH B 6 235 235 HOH HOH . F 3 HOH B 7 236 15 HOH HOH . F 3 HOH B 8 237 237 HOH HOH . F 3 HOH B 9 238 22 HOH HOH . F 3 HOH B 10 239 23 HOH HOH . F 3 HOH B 11 240 240 HOH HOH . F 3 HOH B 12 241 241 HOH HOH . F 3 HOH B 13 242 24 HOH HOH . F 3 HOH B 14 243 243 HOH HOH . F 3 HOH B 15 244 26 HOH HOH . F 3 HOH B 16 245 33 HOH HOH . F 3 HOH B 17 246 246 HOH HOH . F 3 HOH B 18 247 247 HOH HOH . F 3 HOH B 19 248 248 HOH HOH . F 3 HOH B 20 249 249 HOH HOH . F 3 HOH B 21 250 34 HOH HOH . F 3 HOH B 22 251 251 HOH HOH . F 3 HOH B 23 252 252 HOH HOH . F 3 HOH B 24 253 35 HOH HOH . F 3 HOH B 25 254 254 HOH HOH . F 3 HOH B 26 255 36 HOH HOH . F 3 HOH B 27 256 37 HOH HOH . F 3 HOH B 28 257 38 HOH HOH . F 3 HOH B 29 258 258 HOH HOH . F 3 HOH B 30 259 39 HOH HOH . F 3 HOH B 31 260 40 HOH HOH . F 3 HOH B 32 261 261 HOH HOH . F 3 HOH B 33 262 46 HOH HOH . F 3 HOH B 34 263 263 HOH HOH . F 3 HOH B 35 264 47 HOH HOH . F 3 HOH B 36 265 265 HOH HOH . F 3 HOH B 37 266 52 HOH HOH . F 3 HOH B 38 267 267 HOH HOH . F 3 HOH B 39 268 268 HOH HOH . F 3 HOH B 40 269 269 HOH HOH . F 3 HOH B 41 270 54 HOH HOH . F 3 HOH B 42 271 56 HOH HOH . F 3 HOH B 43 272 272 HOH HOH . F 3 HOH B 44 273 273 HOH HOH . F 3 HOH B 45 274 57 HOH HOH . F 3 HOH B 46 275 58 HOH HOH . F 3 HOH B 47 276 59 HOH HOH . F 3 HOH B 48 277 277 HOH HOH . F 3 HOH B 49 278 63 HOH HOH . F 3 HOH B 50 279 65 HOH HOH . F 3 HOH B 51 280 280 HOH HOH . F 3 HOH B 52 281 68 HOH HOH . F 3 HOH B 53 282 71 HOH HOH . F 3 HOH B 54 283 74 HOH HOH . F 3 HOH B 55 284 75 HOH HOH . F 3 HOH B 56 285 77 HOH HOH . F 3 HOH B 57 286 80 HOH HOH . F 3 HOH B 58 287 81 HOH HOH . F 3 HOH B 59 288 84 HOH HOH . F 3 HOH B 60 289 85 HOH HOH . F 3 HOH B 61 290 90 HOH HOH . F 3 HOH B 62 291 91 HOH HOH . F 3 HOH B 63 292 94 HOH HOH . F 3 HOH B 64 293 96 HOH HOH . F 3 HOH B 65 294 99 HOH HOH . F 3 HOH B 66 295 102 HOH HOH . F 3 HOH B 67 296 103 HOH HOH . F 3 HOH B 68 297 104 HOH HOH . F 3 HOH B 69 298 107 HOH HOH . F 3 HOH B 70 299 112 HOH HOH . F 3 HOH B 71 300 118 HOH HOH . F 3 HOH B 72 301 119 HOH HOH . F 3 HOH B 73 302 120 HOH HOH . F 3 HOH B 74 303 130 HOH HOH . F 3 HOH B 75 304 122 HOH HOH . F 3 HOH B 76 305 123 HOH HOH . F 3 HOH B 77 306 124 HOH HOH . F 3 HOH B 78 307 125 HOH HOH . F 3 HOH B 79 308 127 HOH HOH . F 3 HOH B 80 309 128 HOH HOH . F 3 HOH B 81 310 131 HOH HOH . F 3 HOH B 82 311 135 HOH HOH . F 3 HOH B 83 312 142 HOH HOH . F 3 HOH B 84 313 143 HOH HOH . F 3 HOH B 85 314 149 HOH HOH . F 3 HOH B 86 315 151 HOH HOH . F 3 HOH B 87 316 152 HOH HOH . F 3 HOH B 88 317 154 HOH HOH . F 3 HOH B 89 318 155 HOH HOH . F 3 HOH B 90 319 156 HOH HOH . F 3 HOH B 91 320 157 HOH HOH . F 3 HOH B 92 321 158 HOH HOH . F 3 HOH B 93 322 159 HOH HOH . F 3 HOH B 94 323 160 HOH HOH . F 3 HOH B 95 324 174 HOH HOH . F 3 HOH B 96 325 162 HOH HOH . F 3 HOH B 97 326 164 HOH HOH . F 3 HOH B 98 327 168 HOH HOH . F 3 HOH B 99 328 169 HOH HOH . F 3 HOH B 100 329 170 HOH HOH . F 3 HOH B 101 330 173 HOH HOH . F 3 HOH B 102 331 175 HOH HOH . F 3 HOH B 103 332 181 HOH HOH . F 3 HOH B 104 333 183 HOH HOH . F 3 HOH B 105 334 186 HOH HOH . F 3 HOH B 106 335 188 HOH HOH . F 3 HOH B 107 336 189 HOH HOH . F 3 HOH B 108 337 191 HOH HOH . F 3 HOH B 109 338 195 HOH HOH . F 3 HOH B 110 339 197 HOH HOH . F 3 HOH B 111 340 198 HOH HOH . F 3 HOH B 112 341 204 HOH HOH . F 3 HOH B 113 342 206 HOH HOH . F 3 HOH B 114 343 208 HOH HOH . F 3 HOH B 115 344 211 HOH HOH . F 3 HOH B 116 345 212 HOH HOH . F 3 HOH B 117 346 214 HOH HOH . F 3 HOH B 118 347 219 HOH HOH . F 3 HOH B 119 348 227 HOH HOH . F 3 HOH B 120 349 229 HOH HOH . F 3 HOH B 121 350 51 HOH HOH . F 3 HOH B 122 351 121 HOH HOH . F 3 HOH B 123 352 161 HOH HOH . F 3 HOH B 124 353 217 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 N N1 U5P . . . D 2 -1.151 -1.023 20.418 1 8.36 ? N1 U5P 229 B 1 HETATM 2 C C2 U5P . . . D 2 -2.243 -0.235 19.93 1 10.14 ? C2 U5P 229 B 1 HETATM 3 N N3 U5P . . . D 2 -2.542 -0.433 18.583 1 7.3 ? N3 U5P 229 B 1 HETATM 4 C C4 U5P . . . D 2 -1.952 -1.367 17.702 1 9.74 ? C4 U5P 229 B 1 HETATM 5 C C5 U5P . . . D 2 -0.885 -2.162 18.281 1 8.15 ? C5 U5P 229 B 1 HETATM 6 C C6 U5P . . . D 2 -0.538 -1.985 19.574 1 9.55 ? C6 U5P 229 B 1 HETATM 7 O O2 U5P . . . D 2 -2.853 0.525 20.651 1 11.17 ? O2 U5P 229 B 1 HETATM 8 O O4 U5P . . . D 2 -2.377 -1.436 16.57 1 11.66 ? O4 U5P 229 B 1 HETATM 9 C C1' U5P . . . D 2 -0.64 -0.894 21.797 1 7.45 ? C1' U5P 229 B 1 HETATM 10 C C2' U5P . . . D 2 -0.23 0.469 22.296 1 10.28 ? C2' U5P 229 B 1 HETATM 11 O O2' U5P . . . D 2 1.128 0.807 22.026 1 11.66 ? O2' U5P 229 B 1 HETATM 12 C C3' U5P . . . D 2 -0.532 0.387 23.754 1 9.82 ? C3' U5P 229 B 1 HETATM 13 C C4' U5P . . . D 2 -1.788 -0.484 23.821 1 7.66 ? C4' U5P 229 B 1 HETATM 14 O O3' U5P . . . D 2 0.562 -0.188 24.48 1 10.51 ? O3' U5P 229 B 1 HETATM 15 O O4' U5P . . . D 2 -1.656 -1.348 22.663 1 7.88 ? O4' U5P 229 B 1 HETATM 16 C C5' U5P . . . D 2 -3.144 0.205 23.782 1 9.35 ? C5' U5P 229 B 1 HETATM 17 O O5' U5P . . . D 2 -3.293 0.942 25.011 1 9.35 ? O5' U5P 229 B 1 HETATM 18 P P U5P . . . D 2 -4.619 1.716 25.366 1 9.07 ? P U5P 229 B 1 HETATM 19 O O1P U5P . . . D 2 -5.129 2.471 24.173 1 10.11 ? O1P U5P 229 B 1 HETATM 20 O O2P U5P . . . D 2 -4.218 2.651 26.462 1 8.6 ? O2P U5P 229 B 1 HETATM 21 O O3P U5P . . . D 2 -5.673 0.678 25.956 1 11.32 ? O3P U5P 229 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #