data_4N3A # _model_server_result.job_id vRZbzC0piw7qahnQaflkmw _model_server_result.datetime_utc '2024-11-06 17:38:18' _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 4n3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1201}' # _entry.id 4N3A # _exptl.entry_id 4N3A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 120 _cell.entry_id 4N3A _cell.length_a 98.929 _cell.length_b 98.929 _cell.length_c 367.015 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N3A _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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 # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 UDP sing 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 4N3A _atom_sites.fract_transf_matrix[1][1] 0.010108 _atom_sites.fract_transf_matrix[1][2] 0.005836 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011672 _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] 0.002725 _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 3 UDP A 1 1201 1201 UDP UDP . D 4 HOH A 1 1301 1 HOH HOH . D 4 HOH A 2 1302 2 HOH HOH . D 4 HOH A 3 1303 3 HOH HOH . D 4 HOH A 4 1304 4 HOH HOH . D 4 HOH A 5 1305 5 HOH HOH . D 4 HOH A 6 1306 6 HOH HOH . D 4 HOH A 7 1307 7 HOH HOH . D 4 HOH A 8 1308 8 HOH HOH . D 4 HOH A 9 1309 9 HOH HOH . D 4 HOH A 10 1310 10 HOH HOH . D 4 HOH A 11 1311 11 HOH HOH . D 4 HOH A 12 1312 12 HOH HOH . D 4 HOH A 13 1313 13 HOH HOH . D 4 HOH A 14 1314 14 HOH HOH . D 4 HOH A 15 1315 15 HOH HOH . D 4 HOH A 16 1316 17 HOH HOH . D 4 HOH A 17 1317 18 HOH HOH . D 4 HOH A 18 1318 20 HOH HOH . D 4 HOH A 19 1319 21 HOH HOH . D 4 HOH A 20 1320 22 HOH HOH . D 4 HOH A 21 1321 23 HOH HOH . D 4 HOH A 22 1322 24 HOH HOH . D 4 HOH A 23 1323 25 HOH HOH . D 4 HOH A 24 1324 26 HOH HOH . D 4 HOH A 25 1325 27 HOH HOH . D 4 HOH A 26 1326 28 HOH HOH . D 4 HOH A 27 1327 29 HOH HOH . D 4 HOH A 28 1328 30 HOH HOH . D 4 HOH A 29 1329 32 HOH HOH . D 4 HOH A 30 1330 33 HOH HOH . D 4 HOH A 31 1331 34 HOH HOH . D 4 HOH A 32 1332 35 HOH HOH . D 4 HOH A 33 1333 36 HOH HOH . D 4 HOH A 34 1334 37 HOH HOH . D 4 HOH A 35 1335 38 HOH HOH . D 4 HOH A 36 1336 39 HOH HOH . D 4 HOH A 37 1337 40 HOH HOH . D 4 HOH A 38 1338 41 HOH HOH . D 4 HOH A 39 1339 42 HOH HOH . D 4 HOH A 40 1340 43 HOH HOH . D 4 HOH A 41 1341 44 HOH HOH . D 4 HOH A 42 1342 45 HOH HOH . D 4 HOH A 43 1343 46 HOH HOH . D 4 HOH A 44 1344 47 HOH HOH . D 4 HOH A 45 1345 48 HOH HOH . D 4 HOH A 46 1346 49 HOH HOH . D 4 HOH A 47 1347 50 HOH HOH . D 4 HOH A 48 1348 51 HOH HOH . D 4 HOH A 49 1349 52 HOH HOH . D 4 HOH A 50 1350 53 HOH HOH . D 4 HOH A 51 1351 54 HOH HOH . D 4 HOH A 52 1352 55 HOH HOH . D 4 HOH A 53 1353 56 HOH HOH . D 4 HOH A 54 1354 57 HOH HOH . D 4 HOH A 55 1355 58 HOH HOH . D 4 HOH A 56 1356 60 HOH HOH . D 4 HOH A 57 1357 61 HOH HOH . D 4 HOH A 58 1358 62 HOH HOH . D 4 HOH A 59 1359 63 HOH HOH . D 4 HOH A 60 1360 64 HOH HOH . D 4 HOH A 61 1361 65 HOH HOH . D 4 HOH A 62 1362 66 HOH HOH . D 4 HOH A 63 1363 67 HOH HOH . D 4 HOH A 64 1364 68 HOH HOH . D 4 HOH A 65 1365 69 HOH HOH . D 4 HOH A 66 1366 70 HOH HOH . D 4 HOH A 67 1367 71 HOH HOH . D 4 HOH A 68 1368 72 HOH HOH . D 4 HOH A 69 1369 73 HOH HOH . D 4 HOH A 70 1370 74 HOH HOH . D 4 HOH A 71 1371 75 HOH HOH . D 4 HOH A 72 1372 76 HOH HOH . D 4 HOH A 73 1373 77 HOH HOH . D 4 HOH A 74 1374 78 HOH HOH . D 4 HOH A 75 1375 79 HOH HOH . D 4 HOH A 76 1376 80 HOH HOH . D 4 HOH A 77 1377 81 HOH HOH . D 4 HOH A 78 1378 82 HOH HOH . D 4 HOH A 79 1379 83 HOH HOH . D 4 HOH A 80 1380 84 HOH HOH . D 4 HOH A 81 1381 85 HOH HOH . D 4 HOH A 82 1382 86 HOH HOH . D 4 HOH A 83 1383 87 HOH HOH . D 4 HOH A 84 1384 88 HOH HOH . D 4 HOH A 85 1385 89 HOH HOH . D 4 HOH A 86 1386 90 HOH HOH . D 4 HOH A 87 1387 91 HOH HOH . D 4 HOH A 88 1388 92 HOH HOH . D 4 HOH A 89 1389 93 HOH HOH . D 4 HOH A 90 1390 95 HOH HOH . D 4 HOH A 91 1391 96 HOH HOH . D 4 HOH A 92 1392 97 HOH HOH . D 4 HOH A 93 1393 98 HOH HOH . D 4 HOH A 94 1394 99 HOH HOH . D 4 HOH A 95 1395 100 HOH HOH . D 4 HOH A 96 1396 101 HOH HOH . D 4 HOH A 97 1397 102 HOH HOH . D 4 HOH A 98 1398 103 HOH HOH . D 4 HOH A 99 1399 104 HOH HOH . D 4 HOH A 100 1400 105 HOH HOH . D 4 HOH A 101 1401 106 HOH HOH . D 4 HOH A 102 1402 107 HOH HOH . D 4 HOH A 103 1403 108 HOH HOH . D 4 HOH A 104 1404 109 HOH HOH . D 4 HOH A 105 1405 110 HOH HOH . D 4 HOH A 106 1406 111 HOH HOH . D 4 HOH A 107 1407 112 HOH HOH . D 4 HOH A 108 1408 113 HOH HOH . D 4 HOH A 109 1409 114 HOH HOH . D 4 HOH A 110 1410 115 HOH HOH . D 4 HOH A 111 1411 116 HOH HOH . D 4 HOH A 112 1412 117 HOH HOH . D 4 HOH A 113 1413 118 HOH HOH . D 4 HOH A 114 1414 119 HOH HOH . D 4 HOH A 115 1415 120 HOH HOH . D 4 HOH A 116 1416 121 HOH HOH . D 4 HOH A 117 1417 122 HOH HOH . D 4 HOH A 118 1418 123 HOH HOH . D 4 HOH A 119 1419 124 HOH HOH . D 4 HOH A 120 1420 125 HOH HOH . D 4 HOH A 121 1421 126 HOH HOH . D 4 HOH A 122 1422 127 HOH HOH . D 4 HOH A 123 1423 128 HOH HOH . D 4 HOH A 124 1424 129 HOH HOH . D 4 HOH A 125 1425 130 HOH HOH . D 4 HOH A 126 1426 131 HOH HOH . D 4 HOH A 127 1427 132 HOH HOH . D 4 HOH A 128 1428 133 HOH HOH . D 4 HOH A 129 1429 134 HOH HOH . D 4 HOH A 130 1430 135 HOH HOH . D 4 HOH A 131 1431 136 HOH HOH . D 4 HOH A 132 1432 137 HOH HOH . D 4 HOH A 133 1433 138 HOH HOH . D 4 HOH A 134 1434 140 HOH HOH . D 4 HOH A 135 1435 141 HOH HOH . D 4 HOH A 136 1436 142 HOH HOH . D 4 HOH A 137 1437 143 HOH HOH . D 4 HOH A 138 1438 144 HOH HOH . D 4 HOH A 139 1439 145 HOH HOH . D 4 HOH A 140 1440 148 HOH HOH . E 4 HOH B 1 101 16 HOH HOH . E 4 HOH B 2 102 19 HOH HOH . E 4 HOH B 3 103 31 HOH HOH . E 4 HOH B 4 104 59 HOH HOH . E 4 HOH B 5 105 94 HOH HOH . E 4 HOH B 6 106 139 HOH HOH . E 4 HOH B 7 107 146 HOH HOH . E 4 HOH B 8 108 147 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 UDP . . . C 3 1.409 -45.933 11.915 1 23.4 ? N1 UDP 1201 A 1 HETATM 2 C C2 UDP . . . C 3 2.41 -46.857 11.68 1 22.59 ? C2 UDP 1201 A 1 HETATM 3 N N3 UDP . . . C 3 2.163 -47.96 10.9 1 21.3 ? N3 UDP 1201 A 1 HETATM 4 C C4 UDP . . . C 3 0.897 -48.153 10.377 1 20.32 ? C4 UDP 1201 A 1 HETATM 5 C C5 UDP . . . C 3 -0.125 -47.241 10.626 1 19.18 ? C5 UDP 1201 A 1 HETATM 6 C C6 UDP . . . C 3 0.148 -46.108 11.391 1 17.05 ? C6 UDP 1201 A 1 HETATM 7 O O2 UDP . . . C 3 3.543 -46.693 12.147 1 24.12 ? O2 UDP 1201 A 1 HETATM 8 O O4 UDP . . . C 3 0.701 -49.134 9.679 1 21.89 ? O4 UDP 1201 A 1 HETATM 9 C C1' UDP . . . C 3 1.736 -44.802 12.811 1 24.06 ? C1' UDP 1201 A 1 HETATM 10 C C2' UDP . . . C 3 1.41 -43.398 12.345 1 24.77 ? C2' UDP 1201 A 1 HETATM 11 O O2' UDP . . . C 3 2.438 -42.787 11.576 1 20.69 ? O2' UDP 1201 A 1 HETATM 12 C C3' UDP . . . C 3 1.209 -42.681 13.668 1 27.54 ? C3' UDP 1201 A 1 HETATM 13 C C4' UDP . . . C 3 0.693 -43.768 14.598 1 26.81 ? C4' UDP 1201 A 1 HETATM 14 O O4' UDP . . . C 3 0.993 -45.01 13.994 1 23.7 ? O4' UDP 1201 A 1 HETATM 15 O O3' UDP . . . C 3 2.464 -42.278 14.168 1 26.05 ? O3' UDP 1201 A 1 HETATM 16 C C5' UDP . . . C 3 -0.802 -43.661 14.852 1 20.23 ? C5' UDP 1201 A 1 HETATM 17 O O5' UDP . . . C 3 -0.986 -42.727 15.902 1 22.89 ? O5' UDP 1201 A 1 HETATM 18 P PA UDP . . . C 3 -2.313 -41.795 16.015 1 23.39 ? PA UDP 1201 A 1 HETATM 19 O O1A UDP . . . C 3 -2.219 -40.974 17.235 1 19.79 ? O1A UDP 1201 A 1 HETATM 20 O O2A UDP . . . C 3 -3.471 -42.717 16.041 1 24.29 ? O2A UDP 1201 A 1 HETATM 21 O O3A UDP . . . C 3 -2.211 -40.885 14.71 1 21.81 ? O3A UDP 1201 A 1 HETATM 22 P PB UDP . . . C 3 -3.025 -39.526 14.427 1 23.4 ? PB UDP 1201 A 1 HETATM 23 O O1B UDP . . . C 3 -4.274 -39.582 15.183 1 25.04 ? O1B UDP 1201 A 1 HETATM 24 O O2B UDP . . . C 3 -3.222 -39.483 12.966 1 19.98 ? O2B UDP 1201 A 1 HETATM 25 O O3B UDP . . . C 3 -2.193 -38.367 14.864 1 21.41 ? O3B UDP 1201 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #