data_3CKV # _model_server_result.job_id i4_VhTEJjuBEGNo-m6Jp8w _model_server_result.datetime_utc '2024-10-20 08:19:48' _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 3ckv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":331}' # _entry.id 3CKV # _exptl.entry_id 3CKV _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 90 _cell.entry_id 3CKV _cell.length_a 86.967 _cell.length_b 86.967 _cell.length_c 103.932 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CKV _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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,F _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 375 n n N1 C6 UDP sing 376 n n N1 C1' UDP sing 377 n n C2 N3 UDP sing 378 n n C2 O2 UDP doub 379 n n N3 C4 UDP sing 380 n n N3 HN3 UDP sing 381 n n C4 C5 UDP sing 382 n n C4 O4 UDP doub 383 n n C5 C6 UDP doub 384 n n C5 H5 UDP sing 385 n n C6 H6 UDP sing 386 n n C1' C2' UDP sing 387 n n C1' O4' UDP sing 388 n n C1' H1' UDP sing 389 n n C2' O2' UDP sing 390 n n C2' C3' UDP sing 391 n n C2' H2' UDP sing 392 n n O2' HO2' UDP sing 393 n n C3' C4' UDP sing 394 n n C3' O3' UDP sing 395 n n C3' H3' UDP sing 396 n n C4' O4' UDP sing 397 n n C4' C5' UDP sing 398 n n C4' H4' UDP sing 399 n n O3' HO3' UDP sing 400 n n C5' O5' UDP sing 401 n n C5' "H5'1" UDP sing 402 n n C5' "H5'2" UDP sing 403 n n O5' PA UDP sing 404 n n PA O1A UDP doub 405 n n PA O2A UDP sing 406 n n PA O3A UDP sing 407 n n O2A HOA2 UDP sing 408 n n O3A PB UDP sing 409 n n PB O1B UDP doub 410 n n PB O2B UDP sing 411 n n PB O3B UDP sing 412 n n O2B HOB2 UDP sing 413 n n O3B HOB3 UDP sing 414 n n # _atom_sites.entry_id 3CKV _atom_sites.fract_transf_matrix[1][1] 0.011499 _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] 0.011499 _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] 0.009622 _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 SO4 A 1 330 1 SO4 SO4 . C 3 UDP A 1 331 1 UDP UDP . D 4 GOL A 1 332 1 GOL GOL . E 4 GOL A 1 333 2 GOL GOL . F 5 HOH A 1 334 1 HOH HOH . F 5 HOH A 2 335 2 HOH HOH . F 5 HOH A 3 336 3 HOH HOH . F 5 HOH A 4 337 4 HOH HOH . F 5 HOH A 5 338 5 HOH HOH . F 5 HOH A 6 339 6 HOH HOH . F 5 HOH A 7 340 7 HOH HOH . F 5 HOH A 8 341 8 HOH HOH . F 5 HOH A 9 342 9 HOH HOH . F 5 HOH A 10 343 10 HOH HOH . F 5 HOH A 11 344 11 HOH HOH . F 5 HOH A 12 345 12 HOH HOH . F 5 HOH A 13 346 13 HOH HOH . F 5 HOH A 14 347 14 HOH HOH . F 5 HOH A 15 348 15 HOH HOH . F 5 HOH A 16 349 16 HOH HOH . F 5 HOH A 17 350 17 HOH HOH . F 5 HOH A 18 351 18 HOH HOH . F 5 HOH A 19 352 19 HOH HOH . F 5 HOH A 20 353 20 HOH HOH . F 5 HOH A 21 354 21 HOH HOH . F 5 HOH A 22 355 22 HOH HOH . F 5 HOH A 23 356 23 HOH HOH . F 5 HOH A 24 357 24 HOH HOH . F 5 HOH A 25 358 25 HOH HOH . F 5 HOH A 26 359 26 HOH HOH . F 5 HOH A 27 360 27 HOH HOH . F 5 HOH A 28 361 28 HOH HOH . F 5 HOH A 29 362 29 HOH HOH . F 5 HOH A 30 363 30 HOH HOH . F 5 HOH A 31 364 31 HOH HOH . F 5 HOH A 32 365 32 HOH HOH . F 5 HOH A 33 366 33 HOH HOH . F 5 HOH A 34 367 34 HOH HOH . F 5 HOH A 35 368 35 HOH HOH . F 5 HOH A 36 369 36 HOH HOH . F 5 HOH A 37 370 37 HOH HOH . F 5 HOH A 38 371 38 HOH HOH . F 5 HOH A 39 372 39 HOH HOH . F 5 HOH A 40 373 40 HOH HOH . F 5 HOH A 41 374 41 HOH HOH . F 5 HOH A 42 375 42 HOH HOH . F 5 HOH A 43 376 43 HOH HOH . F 5 HOH A 44 377 44 HOH HOH . F 5 HOH A 45 378 45 HOH HOH . F 5 HOH A 46 379 46 HOH HOH . F 5 HOH A 47 380 47 HOH HOH . F 5 HOH A 48 381 48 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 6.828 27.49 15.048 1 34.54 ? N1 UDP 331 A 1 HETATM 2 C C2 UDP . . . C 3 6.693 28.736 15.671 1 33.64 ? C2 UDP 331 A 1 HETATM 3 N N3 UDP . . . C 3 6.621 29.896 14.911 1 33.38 ? N3 UDP 331 A 1 HETATM 4 C C4 UDP . . . C 3 6.669 29.844 13.532 1 32.82 ? C4 UDP 331 A 1 HETATM 5 C C5 UDP . . . C 3 6.808 28.602 12.885 1 33.69 ? C5 UDP 331 A 1 HETATM 6 C C6 UDP . . . C 3 7.026 27.452 13.675 1 32.51 ? C6 UDP 331 A 1 HETATM 7 O O2 UDP . . . C 3 6.642 28.859 16.903 1 33.31 ? O2 UDP 331 A 1 HETATM 8 O O4 UDP . . . C 3 6.583 30.919 12.911 1 33.35 ? O4 UDP 331 A 1 HETATM 9 C C1' UDP . . . C 3 6.915 26.255 15.878 1 35.59 ? C1' UDP 331 A 1 HETATM 10 C C2' UDP . . . C 3 5.949 25.156 15.417 1 38.41 ? C2' UDP 331 A 1 HETATM 11 O O2' UDP . . . C 3 4.66 25.278 15.987 1 36.36 ? O2' UDP 331 A 1 HETATM 12 C C3' UDP . . . C 3 6.675 23.883 15.839 1 39.67 ? C3' UDP 331 A 1 HETATM 13 C C4' UDP . . . C 3 8.141 24.227 15.648 1 41.29 ? C4' UDP 331 A 1 HETATM 14 O O4' UDP . . . C 3 8.205 25.661 15.753 1 40.51 ? O4' UDP 331 A 1 HETATM 15 O O3' UDP . . . C 3 6.506 23.616 17.217 1 41.26 ? O3' UDP 331 A 1 HETATM 16 C C5' UDP . . . C 3 8.68 23.726 14.299 1 45.1 ? C5' UDP 331 A 1 HETATM 17 O O5' UDP . . . C 3 7.931 24.291 13.231 1 52.72 ? O5' UDP 331 A 1 HETATM 18 P PA UDP . . . C 3 7.824 23.62 11.749 1 57.84 ? PA UDP 331 A 1 HETATM 19 O O1A UDP . . . C 3 7.146 24.57 10.8 1 57.87 ? O1A UDP 331 A 1 HETATM 20 O O2A UDP . . . C 3 7.088 22.327 11.808 1 57.95 ? O2A UDP 331 A 1 HETATM 21 O O3A UDP . . . C 3 9.381 23.381 11.387 1 58.57 ? O3A UDP 331 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #