data_3BNZ # _model_server_result.job_id stwihihHNW7v20TfjHP17g _model_server_result.datetime_utc '2024-11-26 20:09:11' _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 3bnz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":317}' # _entry.id 3BNZ # _exptl.entry_id 3BNZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 3BNZ _cell.length_a 76.563 _cell.length_b 76.563 _cell.length_c 213.073 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BNZ _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 1,2 # 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' 10_554 -y,-x,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -35.512167 # _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 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 394 n n N1 C6 UMP sing 395 n n N1 C1' UMP sing 396 n n C2 N3 UMP sing 397 n n C2 O2 UMP doub 398 n n N3 C4 UMP sing 399 n n N3 HN3 UMP sing 400 n n C4 C5 UMP sing 401 n n C4 O4 UMP doub 402 n n C5 C6 UMP doub 403 n n C5 H5 UMP sing 404 n n C6 H6 UMP sing 405 n n C1' C2' UMP sing 406 n n C1' O4' UMP sing 407 n n C1' H1' UMP sing 408 n n C2' C3' UMP sing 409 n n C2' H2' UMP sing 410 n n C2' "H2''" UMP sing 411 n n C3' C4' UMP sing 412 n n C3' O3' UMP sing 413 n n C3' H3' UMP sing 414 n n C4' O4' UMP sing 415 n n C4' C5' UMP sing 416 n n C4' H4' UMP sing 417 n n O3' HO3' UMP sing 418 n n C5' O5' UMP sing 419 n n C5' H5' UMP sing 420 n n C5' "H5''" UMP sing 421 n n O5' P UMP sing 422 n n P OP1 UMP doub 423 n n P OP2 UMP sing 424 n n P OP3 UMP sing 425 n n OP2 HOP2 UMP sing 426 n n OP3 HOP3 UMP sing 427 n n # _atom_sites.entry_id 3BNZ _atom_sites.fract_transf_matrix[1][1] 0.013061 _atom_sites.fract_transf_matrix[1][2] 0.007541 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015082 _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] 0.004693 _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 PO4 A 1 319 1 PO4 PO4 . C 3 UMP A 1 317 317 UMP UMP . D 4 C16 A 1 318 318 C16 C16 . E 5 HOH A 1 320 1 HOH HOH . E 5 HOH A 2 321 2 HOH HOH . E 5 HOH A 3 322 3 HOH HOH . E 5 HOH A 4 323 4 HOH HOH . E 5 HOH A 5 324 5 HOH HOH . E 5 HOH A 6 325 6 HOH HOH . E 5 HOH A 7 326 7 HOH HOH . E 5 HOH A 8 327 8 HOH HOH . E 5 HOH A 9 328 9 HOH HOH . E 5 HOH A 10 329 10 HOH HOH . E 5 HOH A 11 330 11 HOH HOH . E 5 HOH A 12 331 12 HOH HOH . E 5 HOH A 13 332 13 HOH HOH . E 5 HOH A 14 333 14 HOH HOH . E 5 HOH A 15 334 15 HOH HOH . E 5 HOH A 16 335 16 HOH HOH . E 5 HOH A 17 336 17 HOH HOH . E 5 HOH A 18 337 18 HOH HOH . E 5 HOH A 19 338 19 HOH HOH . E 5 HOH A 20 339 20 HOH HOH . E 5 HOH A 21 340 21 HOH HOH . E 5 HOH A 22 341 22 HOH HOH . E 5 HOH A 23 342 23 HOH HOH . E 5 HOH A 24 343 24 HOH HOH . E 5 HOH A 25 344 25 HOH HOH . E 5 HOH A 26 345 26 HOH HOH . E 5 HOH A 27 346 27 HOH HOH . E 5 HOH A 28 347 28 HOH HOH . E 5 HOH A 29 348 29 HOH HOH . E 5 HOH A 30 349 30 HOH HOH . E 5 HOH A 31 350 31 HOH HOH . E 5 HOH A 32 351 32 HOH HOH . E 5 HOH A 33 352 33 HOH HOH . E 5 HOH A 34 353 34 HOH HOH . E 5 HOH A 35 354 35 HOH HOH . E 5 HOH A 36 355 36 HOH HOH . E 5 HOH A 37 356 37 HOH HOH . E 5 HOH A 38 357 38 HOH HOH . E 5 HOH A 39 358 39 HOH HOH . E 5 HOH A 40 359 40 HOH HOH . E 5 HOH A 41 360 41 HOH HOH . E 5 HOH A 42 361 42 HOH HOH . E 5 HOH A 43 362 43 HOH HOH . E 5 HOH A 44 363 44 HOH HOH . E 5 HOH A 45 364 45 HOH HOH . E 5 HOH A 46 365 46 HOH HOH . E 5 HOH A 47 366 47 HOH HOH . E 5 HOH A 48 367 48 HOH HOH . E 5 HOH A 49 368 49 HOH HOH . E 5 HOH A 50 369 50 HOH HOH . E 5 HOH A 51 370 51 HOH HOH . E 5 HOH A 52 371 52 HOH HOH . E 5 HOH A 53 372 53 HOH HOH . E 5 HOH A 54 373 54 HOH HOH . E 5 HOH A 55 374 55 HOH HOH . E 5 HOH A 56 375 56 HOH HOH . E 5 HOH A 57 376 57 HOH HOH . E 5 HOH A 58 377 58 HOH HOH . E 5 HOH A 59 378 59 HOH HOH . E 5 HOH A 60 379 60 HOH HOH . E 5 HOH A 61 380 61 HOH HOH . E 5 HOH A 62 381 62 HOH HOH . E 5 HOH A 63 382 63 HOH HOH . E 5 HOH A 64 383 64 HOH HOH . E 5 HOH A 65 384 65 HOH HOH . E 5 HOH A 66 385 66 HOH HOH . E 5 HOH A 67 386 67 HOH HOH . E 5 HOH A 68 387 68 HOH HOH . E 5 HOH A 69 388 69 HOH HOH . E 5 HOH A 70 389 70 HOH HOH . E 5 HOH A 71 390 71 HOH HOH . E 5 HOH A 72 391 72 HOH HOH . E 5 HOH A 73 392 73 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 UMP . . . C 3 -27.545 34 -14.005 1 42.74 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . C 3 -26.977 32.985 -13.237 1 42.58 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . C 3 -27.598 32.52 -12.11 1 43.93 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . C 3 -28.802 33.068 -11.691 1 45.31 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . C 3 -29.388 34.103 -12.452 1 45.14 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . C 3 -28.732 34.563 -13.611 1 43.5 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . C 3 -25.935 32.448 -13.526 1 43.05 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . C 3 -29.336 32.628 -10.657 1 44.39 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . C 3 -26.877 34.51 -15.207 1 41.83 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . C 3 -26.713 33.493 -16.333 1 39.13 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . C 3 -26.453 34.443 -17.488 1 38.03 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . C 3 -27.028 35.786 -17.059 1 38.75 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . C 3 -25.071 34.618 -17.697 1 35.04 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . C 3 -27.603 35.581 -15.78 1 39.73 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . C 3 -28.014 36.352 -18.081 1 40.93 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . C 3 -29.224 35.62 -18.208 1 41.93 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . C 3 -29.753 35.073 -19.648 1 42.59 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . C 3 -31.233 35.356 -19.759 1 39.43 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . C 3 -28.968 35.731 -20.754 1 40.5 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . C 3 -29.514 33.588 -19.757 1 41.68 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 1295 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 20 #