data_2P72 # _model_server_result.job_id zoBNqszrzxMp5YSPKmK2IQ _model_server_result.datetime_utc '2025-02-27 17:23:53' _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 2p72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":215}' # _entry.id 2P72 # _exptl.entry_id 2P72 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 126.56 _cell.angle_gamma 90 _cell.entry_id 2P72 _cell.length_a 126.448 _cell.length_b 61.776 _cell.length_c 76.091 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2P72 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F 1 1 B,D,E,G 2 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 E _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 OD2 ASP 80 A ASP 78 1_555 C MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc2 A OD2 ASP 82 A ASP 80 1_555 C MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc3 A NE2 HIS 195 A HIS 193 1_555 C MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc4 C MN MN . A MN 214 1_555 F O HOH . A HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc5 C MN MN . A MN 214 1_555 F O HOH . A HOH 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc6 B OD2 ASP 80 B ASP 78 1_555 D MN MN . B MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc7 B OD2 ASP 82 B ASP 80 1_555 D MN MN . B MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc8 B NE2 HIS 195 B HIS 193 1_555 D MN MN . B MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc9 D MN MN . B MN 214 1_555 E O1A UPG . B UPG 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc10 D MN MN . B MN 214 1_555 G O HOH . B HOH 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc11 D MN MN . B MN 214 1_555 G O HOH . B HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 UPG sing 358 n n N1 C6 UPG sing 359 n n N1 C1C UPG sing 360 n n C2 N3 UPG sing 361 n n C2 O2 UPG doub 362 n n N3 C4 UPG sing 363 n n N3 HN3 UPG sing 364 n n C4 C5 UPG sing 365 n n C4 O4 UPG doub 366 n n C5 C6 UPG doub 367 n n C5 H5 UPG sing 368 n n C6 H6 UPG sing 369 n n C1C C2C UPG sing 370 n n C1C O4C UPG sing 371 n n C1C H1C UPG sing 372 n n C2C O2C UPG sing 373 n n C2C C3C UPG sing 374 n n C2C H2C UPG sing 375 n n O2C HO2C UPG sing 376 n n C3C C4C UPG sing 377 n n C3C O3C UPG sing 378 n n C3C H3C UPG sing 379 n n C4C O4C UPG sing 380 n n C4C C5C UPG sing 381 n n C4C H4C UPG sing 382 n n O3C HO3C UPG sing 383 n n C5C O5C UPG sing 384 n n C5C H5C1 UPG sing 385 n n C5C H5C2 UPG sing 386 n n O5C PA UPG sing 387 n n PA O1A UPG doub 388 n n PA O2A UPG sing 389 n n PA O3A UPG sing 390 n n O2A HOA2 UPG sing 391 n n O3A PB UPG sing 392 n n PB O1B UPG doub 393 n n PB O2B UPG sing 394 n n PB O3B UPG sing 395 n n O2B HOB2 UPG sing 396 n n O3B C1' UPG sing 397 n n C1' C2' UPG sing 398 n n C1' O5' UPG sing 399 n n C1' H1' UPG sing 400 n n C2' C3' UPG sing 401 n n C2' O2' UPG sing 402 n n C2' H2' UPG sing 403 n n C3' C4' UPG sing 404 n n C3' O3' UPG sing 405 n n C3' H3' UPG sing 406 n n C4' C5' UPG sing 407 n n C4' O4' UPG sing 408 n n C4' H4' UPG sing 409 n n C5' C6' UPG sing 410 n n C5' O5' UPG sing 411 n n C5' H5' UPG sing 412 n n C6' O6' UPG sing 413 n n C6' "H6'1" UPG sing 414 n n C6' "H6'2" UPG sing 415 n n O2' HO2' UPG sing 416 n n O3' HO3' UPG sing 417 n n O4' HO4' UPG sing 418 n n O6' HO6' UPG sing 419 n n # _atom_sites.entry_id 2P72 _atom_sites.fract_transf_matrix[1][1] 0.007908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005865 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016188 _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] 0.016362 _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 MN A 1 214 214 MN MN . D 2 MN B 1 214 214 MN MN . E 3 UPG B 1 215 215 UPG UPG . F 4 HOH A 1 215 215 HOH HOH . F 4 HOH A 2 216 216 HOH HOH . F 4 HOH A 3 217 217 HOH HOH . F 4 HOH A 4 218 218 HOH HOH . F 4 HOH A 5 219 219 HOH HOH . F 4 HOH A 6 220 220 HOH HOH . F 4 HOH A 7 221 221 HOH HOH . F 4 HOH A 8 222 222 HOH HOH . F 4 HOH A 9 223 223 HOH HOH . F 4 HOH A 10 224 224 HOH HOH . F 4 HOH A 11 225 225 HOH HOH . F 4 HOH A 12 226 226 HOH HOH . F 4 HOH A 13 227 227 HOH HOH . F 4 HOH A 14 228 228 HOH HOH . F 4 HOH A 15 229 229 HOH HOH . F 4 HOH A 16 230 230 HOH HOH . F 4 HOH A 17 231 231 HOH HOH . F 4 HOH A 18 232 232 HOH HOH . F 4 HOH A 19 233 233 HOH HOH . F 4 HOH A 20 234 234 HOH HOH . F 4 HOH A 21 235 235 HOH HOH . F 4 HOH A 22 236 236 HOH HOH . F 4 HOH A 23 237 237 HOH HOH . F 4 HOH A 24 238 238 HOH HOH . F 4 HOH A 25 239 239 HOH HOH . F 4 HOH A 26 240 240 HOH HOH . F 4 HOH A 27 241 241 HOH HOH . F 4 HOH A 28 242 242 HOH HOH . F 4 HOH A 29 243 243 HOH HOH . F 4 HOH A 30 244 244 HOH HOH . F 4 HOH A 31 245 245 HOH HOH . F 4 HOH A 32 246 246 HOH HOH . F 4 HOH A 33 247 247 HOH HOH . F 4 HOH A 34 248 248 HOH HOH . F 4 HOH A 35 249 249 HOH HOH . F 4 HOH A 36 250 250 HOH HOH . F 4 HOH A 37 251 251 HOH HOH . F 4 HOH A 38 252 252 HOH HOH . F 4 HOH A 39 253 253 HOH HOH . F 4 HOH A 40 254 254 HOH HOH . F 4 HOH A 41 255 255 HOH HOH . F 4 HOH A 42 256 256 HOH HOH . F 4 HOH A 43 257 257 HOH HOH . F 4 HOH A 44 258 258 HOH HOH . F 4 HOH A 45 259 259 HOH HOH . F 4 HOH A 46 260 260 HOH HOH . F 4 HOH A 47 261 261 HOH HOH . F 4 HOH A 48 262 262 HOH HOH . F 4 HOH A 49 263 263 HOH HOH . F 4 HOH A 50 264 264 HOH HOH . F 4 HOH A 51 265 265 HOH HOH . F 4 HOH A 52 266 266 HOH HOH . F 4 HOH A 53 267 267 HOH HOH . F 4 HOH A 54 268 268 HOH HOH . F 4 HOH A 55 269 269 HOH HOH . F 4 HOH A 56 270 270 HOH HOH . F 4 HOH A 57 271 271 HOH HOH . F 4 HOH A 58 272 272 HOH HOH . F 4 HOH A 59 273 273 HOH HOH . F 4 HOH A 60 274 274 HOH HOH . F 4 HOH A 61 275 275 HOH HOH . F 4 HOH A 62 276 276 HOH HOH . F 4 HOH A 63 277 277 HOH HOH . F 4 HOH A 64 278 278 HOH HOH . F 4 HOH A 65 279 279 HOH HOH . F 4 HOH A 66 280 280 HOH HOH . F 4 HOH A 67 281 281 HOH HOH . F 4 HOH A 68 282 282 HOH HOH . F 4 HOH A 69 283 283 HOH HOH . F 4 HOH A 70 284 284 HOH HOH . G 4 HOH B 1 216 216 HOH HOH . G 4 HOH B 2 217 217 HOH HOH . G 4 HOH B 3 218 218 HOH HOH . G 4 HOH B 4 219 219 HOH HOH . G 4 HOH B 5 220 220 HOH HOH . G 4 HOH B 6 221 221 HOH HOH . G 4 HOH B 7 222 222 HOH HOH . G 4 HOH B 8 223 223 HOH HOH . G 4 HOH B 9 224 224 HOH HOH . G 4 HOH B 10 225 225 HOH HOH . G 4 HOH B 11 226 226 HOH HOH . G 4 HOH B 12 227 227 HOH HOH . G 4 HOH B 13 228 228 HOH HOH . G 4 HOH B 14 229 229 HOH HOH . G 4 HOH B 15 230 230 HOH HOH . G 4 HOH B 16 231 231 HOH HOH . G 4 HOH B 17 232 232 HOH HOH . G 4 HOH B 18 233 233 HOH HOH . G 4 HOH B 19 234 234 HOH HOH . G 4 HOH B 20 235 235 HOH HOH . G 4 HOH B 21 236 236 HOH HOH . G 4 HOH B 22 237 237 HOH HOH . G 4 HOH B 23 238 238 HOH HOH . G 4 HOH B 24 239 239 HOH HOH . G 4 HOH B 25 240 240 HOH HOH . G 4 HOH B 26 241 241 HOH HOH . G 4 HOH B 27 242 242 HOH HOH . G 4 HOH B 28 243 243 HOH HOH . G 4 HOH B 29 244 244 HOH HOH . G 4 HOH B 30 245 245 HOH HOH . G 4 HOH B 31 246 246 HOH HOH . G 4 HOH B 32 247 247 HOH HOH . G 4 HOH B 33 248 248 HOH HOH . G 4 HOH B 34 249 249 HOH HOH . G 4 HOH B 35 250 250 HOH HOH . G 4 HOH B 36 251 251 HOH HOH . G 4 HOH B 37 252 252 HOH HOH . G 4 HOH B 38 253 253 HOH HOH . G 4 HOH B 39 254 254 HOH HOH . G 4 HOH B 40 255 255 HOH HOH . G 4 HOH B 41 256 256 HOH HOH . G 4 HOH B 42 257 257 HOH HOH . G 4 HOH B 43 258 258 HOH HOH . G 4 HOH B 44 259 259 HOH HOH . G 4 HOH B 45 260 260 HOH HOH . G 4 HOH B 46 261 261 HOH HOH . G 4 HOH B 47 262 262 HOH HOH . G 4 HOH B 48 263 263 HOH HOH . G 4 HOH B 49 264 264 HOH HOH . G 4 HOH B 50 265 265 HOH HOH . G 4 HOH B 51 266 266 HOH HOH . G 4 HOH B 52 267 267 HOH HOH . G 4 HOH B 53 268 268 HOH HOH . G 4 HOH B 54 269 269 HOH HOH . G 4 HOH B 55 270 270 HOH HOH . G 4 HOH B 56 271 271 HOH HOH . G 4 HOH B 57 272 272 HOH HOH . G 4 HOH B 58 273 273 HOH HOH . G 4 HOH B 59 274 274 HOH HOH . G 4 HOH B 60 275 275 HOH HOH . G 4 HOH B 61 276 276 HOH HOH . G 4 HOH B 62 277 277 HOH HOH . G 4 HOH B 63 278 278 HOH HOH . G 4 HOH B 64 279 279 HOH HOH . G 4 HOH B 65 280 280 HOH HOH . G 4 HOH B 66 281 281 HOH HOH . G 4 HOH B 67 282 282 HOH HOH . G 4 HOH B 68 283 283 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 UPG . . . E 3 -16.17 30.178 -9.816 1 39.21 ? N1 UPG 215 B 1 HETATM 2 C C2 UPG . . . E 3 -14.963 30.007 -10.53 1 40.07 ? C2 UPG 215 B 1 HETATM 3 N N3 UPG . . . E 3 -14.502 31.009 -11.288 1 40.04 ? N3 UPG 215 B 1 HETATM 4 C C4 UPG . . . E 3 -15.147 32.182 -11.383 1 39.22 ? C4 UPG 215 B 1 HETATM 5 C C5 UPG . . . E 3 -16.347 32.386 -10.69 1 39.35 ? C5 UPG 215 B 1 HETATM 6 C C6 UPG . . . E 3 -16.843 31.346 -9.897 1 39.03 ? C6 UPG 215 B 1 HETATM 7 O O2 UPG . . . E 3 -14.346 28.916 -10.458 1 38.82 ? O2 UPG 215 B 1 HETATM 8 O O4 UPG . . . E 3 -14.662 33.075 -12.122 1 39.88 ? O4 UPG 215 B 1 HETATM 9 C C1C UPG . . . E 3 -16.632 29.044 -9.008 1 39.32 ? C1C UPG 215 B 1 HETATM 10 C C2C UPG . . . E 3 -15.817 28.939 -7.722 1 37.61 ? C2C UPG 215 B 1 HETATM 11 O O2C UPG . . . E 3 -15.415 27.576 -7.537 1 37.27 ? O2C UPG 215 B 1 HETATM 12 C C3C UPG . . . E 3 -16.775 29.413 -6.644 1 36.75 ? C3C UPG 215 B 1 HETATM 13 C C4C UPG . . . E 3 -18.151 29.125 -7.223 1 40.23 ? C4C UPG 215 B 1 HETATM 14 O O4C UPG . . . E 3 -18.01 29.198 -8.646 1 39.98 ? O4C UPG 215 B 1 HETATM 15 O O3C UPG . . . E 3 -16.566 28.826 -5.362 1 35.88 ? O3C UPG 215 B 1 HETATM 16 C C5C UPG . . . E 3 -19.159 30.191 -6.868 1 41.46 ? C5C UPG 215 B 1 HETATM 17 O O5C UPG . . . E 3 -18.685 31.445 -7.379 1 43.09 ? O5C UPG 215 B 1 HETATM 18 P PA UPG . . . E 3 -19.004 32.799 -6.556 1 42.71 ? PA UPG 215 B 1 HETATM 19 O O1A UPG . . . E 3 -19.327 32.505 -5.135 1 39.47 ? O1A UPG 215 B 1 HETATM 20 O O2A UPG . . . E 3 -17.849 33.769 -6.678 1 44.59 ? O2A UPG 215 B 1 HETATM 21 O O3A UPG . . . E 3 -20.279 33.383 -7.346 1 47.29 ? O3A UPG 215 B 1 HETATM 22 P PB UPG . . . E 3 -21.149 34.701 -6.945 1 47.69 ? PB UPG 215 B 1 HETATM 23 O O1B UPG . . . E 3 -20.475 35.632 -5.972 1 39.91 ? O1B UPG 215 B 1 HETATM 24 O O2B UPG . . . E 3 -21.506 35.278 -8.28 1 46.04 ? O2B UPG 215 B 1 HETATM 25 O O3B UPG . . . E 3 -22.428 34.088 -6.202 1 48.02 ? O3B UPG 215 B 1 HETATM 26 C C1' UPG . . . E 3 -23.654 33.908 -6.922 1 47.75 ? C1' UPG 215 B 1 HETATM 27 C C2' UPG . . . E 3 -24.771 34.404 -6.01 1 47 ? C2' UPG 215 B 1 HETATM 28 C C3' UPG . . . E 3 -24.763 33.592 -4.698 1 45.91 ? C3' UPG 215 B 1 HETATM 29 C C4' UPG . . . E 3 -24.787 32.079 -4.949 1 46.32 ? C4' UPG 215 B 1 HETATM 30 C C5' UPG . . . E 3 -23.862 31.636 -6.081 1 45.91 ? C5' UPG 215 B 1 HETATM 31 C C6' UPG . . . E 3 -24.288 30.266 -6.592 1 44.87 ? C6' UPG 215 B 1 HETATM 32 O O2' UPG . . . E 3 -24.458 35.772 -5.761 1 43.92 ? O2' UPG 215 B 1 HETATM 33 O O3' UPG . . . E 3 -25.87 33.908 -3.846 1 43.42 ? O3' UPG 215 B 1 HETATM 34 O O4' UPG . . . E 3 -24.428 31.395 -3.726 1 45.58 ? O4' UPG 215 B 1 HETATM 35 O O5' UPG . . . E 3 -23.851 32.52 -7.223 1 49.5 ? O5' UPG 215 B 1 HETATM 36 O O6' UPG . . . E 3 -23.161 29.578 -7.157 1 40.78 ? O6' UPG 215 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #