data_3TKA # _model_server_result.job_id FS-XNPxxYwaIxgfBtMqbRA _model_server_result.datetime_utc '2024-11-25 23:54:05' _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 3tka # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 3TKA # _exptl.entry_id 3TKA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _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 3TKA _cell.length_a 85.66 _cell.length_b 85.66 _cell.length_c 107.059 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TKA _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _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,G,H,I,J _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' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 85.66 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 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id CTN _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CYTIDINE # 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 O5' C5' CTN sing 70 n n O5' H5' CTN sing 71 n n C5' C4' CTN sing 72 n n C5' "H5'1" CTN sing 73 n n C5' "H5'2" CTN sing 74 n n C4' O4' CTN sing 75 n n C4' C3' CTN sing 76 n n C4' H4' CTN sing 77 n n O4' C1' CTN sing 78 n n C1' N1 CTN sing 79 n n C1' C2' CTN sing 80 n n C1' H1' CTN sing 81 n n N1 C6 CTN sing 82 n y N1 C2 CTN sing 83 n y C6 C5 CTN doub 84 n y C6 H6 CTN sing 85 n n C5 C4 CTN sing 86 n y C5 H5 CTN sing 87 n n C4 N3 CTN doub 88 n y C4 N4 CTN sing 89 n n N3 C2 CTN sing 90 n y C2 O2 CTN doub 91 n n N4 HN41 CTN sing 92 n n N4 HN42 CTN sing 93 n n C2' O2' CTN sing 94 n n C2' C3' CTN sing 95 n n C2' H2' CTN sing 96 n n O2' H1 CTN sing 97 n n C3' O3' CTN sing 98 n n C3' H3' CTN sing 99 n n O3' H2 CTN sing 100 n n # _atom_sites.entry_id 3TKA _atom_sites.fract_transf_matrix[1][1] 0.011674 _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] 0.011674 _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] 0.009341 _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 SAM A 1 400 400 SAM SAM . C 3 CTN A 1 500 500 CTN CR . D 4 SO4 A 1 600 600 SO4 SO4 . E 4 SO4 A 1 601 601 SO4 SO4 . F 4 SO4 A 1 602 602 SO4 SO4 . G 4 SO4 A 1 603 603 SO4 SO4 . H 4 SO4 A 1 604 604 SO4 SO4 . I 5 PG4 A 1 700 700 PG4 PEG . J 6 HOH A 1 314 1 HOH HOH . J 6 HOH A 2 315 2 HOH HOH . J 6 HOH A 3 316 3 HOH HOH . J 6 HOH A 4 317 4 HOH HOH . J 6 HOH A 5 318 5 HOH HOH . J 6 HOH A 6 319 6 HOH HOH . J 6 HOH A 7 320 7 HOH HOH . J 6 HOH A 8 321 8 HOH HOH . J 6 HOH A 9 322 9 HOH HOH . J 6 HOH A 10 323 10 HOH HOH . J 6 HOH A 11 324 11 HOH HOH . J 6 HOH A 12 325 12 HOH HOH . J 6 HOH A 13 326 13 HOH HOH . J 6 HOH A 14 327 14 HOH HOH . J 6 HOH A 15 328 15 HOH HOH . J 6 HOH A 16 329 16 HOH HOH . J 6 HOH A 17 330 17 HOH HOH . J 6 HOH A 18 331 18 HOH HOH . J 6 HOH A 19 332 19 HOH HOH . J 6 HOH A 20 333 20 HOH HOH . J 6 HOH A 21 334 21 HOH HOH . J 6 HOH A 22 335 22 HOH HOH . J 6 HOH A 23 336 23 HOH HOH . J 6 HOH A 24 337 24 HOH HOH . J 6 HOH A 25 338 26 HOH HOH . J 6 HOH A 26 339 27 HOH HOH . J 6 HOH A 27 340 28 HOH HOH . J 6 HOH A 28 341 29 HOH HOH . J 6 HOH A 29 342 30 HOH HOH . J 6 HOH A 30 343 31 HOH HOH . J 6 HOH A 31 344 32 HOH HOH . J 6 HOH A 32 345 33 HOH HOH . J 6 HOH A 33 346 34 HOH HOH . J 6 HOH A 34 347 35 HOH HOH . J 6 HOH A 35 348 36 HOH HOH . J 6 HOH A 36 349 37 HOH HOH . J 6 HOH A 37 350 38 HOH HOH . J 6 HOH A 38 351 39 HOH HOH . J 6 HOH A 39 352 40 HOH HOH . J 6 HOH A 40 353 41 HOH HOH . J 6 HOH A 41 354 42 HOH HOH . J 6 HOH A 42 355 43 HOH HOH . J 6 HOH A 43 356 44 HOH HOH . J 6 HOH A 44 357 45 HOH HOH . J 6 HOH A 45 358 46 HOH HOH . J 6 HOH A 46 359 47 HOH HOH . J 6 HOH A 47 360 48 HOH HOH . J 6 HOH A 48 361 49 HOH HOH . J 6 HOH A 49 362 50 HOH HOH . J 6 HOH A 50 363 51 HOH HOH . J 6 HOH A 51 364 53 HOH HOH . J 6 HOH A 52 365 55 HOH HOH . J 6 HOH A 53 366 56 HOH HOH . J 6 HOH A 54 367 57 HOH HOH . J 6 HOH A 55 368 58 HOH HOH . J 6 HOH A 56 369 59 HOH HOH . J 6 HOH A 57 370 60 HOH HOH . J 6 HOH A 58 371 61 HOH HOH . J 6 HOH A 59 372 62 HOH HOH . J 6 HOH A 60 373 63 HOH HOH . J 6 HOH A 61 374 64 HOH HOH . J 6 HOH A 62 375 65 HOH HOH . J 6 HOH A 63 376 66 HOH HOH . J 6 HOH A 64 377 67 HOH HOH . J 6 HOH A 65 378 68 HOH HOH . J 6 HOH A 66 379 69 HOH HOH . J 6 HOH A 67 380 70 HOH HOH . J 6 HOH A 68 381 71 HOH HOH . J 6 HOH A 69 382 72 HOH HOH . J 6 HOH A 70 383 73 HOH HOH . J 6 HOH A 71 384 74 HOH HOH . J 6 HOH A 72 385 75 HOH HOH . J 6 HOH A 73 386 76 HOH HOH . J 6 HOH A 74 387 77 HOH HOH . J 6 HOH A 75 388 78 HOH HOH . J 6 HOH A 76 389 79 HOH HOH . J 6 HOH A 77 390 80 HOH HOH . J 6 HOH A 78 391 82 HOH HOH . J 6 HOH A 79 392 83 HOH HOH . J 6 HOH A 80 393 84 HOH HOH . J 6 HOH A 81 394 85 HOH HOH . J 6 HOH A 82 395 86 HOH HOH . J 6 HOH A 83 396 87 HOH HOH . J 6 HOH A 84 397 88 HOH HOH . J 6 HOH A 85 398 89 HOH HOH . J 6 HOH A 86 399 90 HOH HOH . J 6 HOH A 87 401 91 HOH HOH . J 6 HOH A 88 402 92 HOH HOH . J 6 HOH A 89 403 93 HOH HOH . J 6 HOH A 90 404 94 HOH HOH . J 6 HOH A 91 405 95 HOH HOH . J 6 HOH A 92 406 96 HOH HOH . J 6 HOH A 93 407 97 HOH HOH . J 6 HOH A 94 408 98 HOH HOH . J 6 HOH A 95 409 99 HOH HOH . J 6 HOH A 96 410 100 HOH HOH . J 6 HOH A 97 411 101 HOH HOH . J 6 HOH A 98 412 102 HOH HOH . J 6 HOH A 99 413 103 HOH HOH . J 6 HOH A 100 414 104 HOH HOH . J 6 HOH A 101 415 105 HOH HOH . J 6 HOH A 102 416 106 HOH HOH . J 6 HOH A 103 417 107 HOH HOH . J 6 HOH A 104 418 108 HOH HOH . J 6 HOH A 105 419 109 HOH HOH . J 6 HOH A 106 420 110 HOH HOH . J 6 HOH A 107 421 111 HOH HOH . J 6 HOH A 108 422 112 HOH HOH . J 6 HOH A 109 423 115 HOH HOH . J 6 HOH A 110 424 116 HOH HOH . J 6 HOH A 111 425 118 HOH HOH . J 6 HOH A 112 426 119 HOH HOH . J 6 HOH A 113 427 120 HOH HOH . J 6 HOH A 114 428 121 HOH HOH . J 6 HOH A 115 429 123 HOH HOH . J 6 HOH A 116 430 124 HOH HOH . J 6 HOH A 117 431 126 HOH HOH . J 6 HOH A 118 432 127 HOH HOH . J 6 HOH A 119 433 128 HOH HOH . J 6 HOH A 120 434 129 HOH HOH . J 6 HOH A 121 435 130 HOH HOH . J 6 HOH A 122 436 131 HOH HOH . J 6 HOH A 123 437 132 HOH HOH . J 6 HOH A 124 438 133 HOH HOH . J 6 HOH A 125 439 134 HOH HOH . J 6 HOH A 126 440 135 HOH HOH . J 6 HOH A 127 441 136 HOH HOH . J 6 HOH A 128 442 137 HOH HOH . J 6 HOH A 129 443 138 HOH HOH . J 6 HOH A 130 444 139 HOH HOH . J 6 HOH A 131 445 140 HOH HOH . J 6 HOH A 132 446 141 HOH HOH . J 6 HOH A 133 447 142 HOH HOH . J 6 HOH A 134 448 143 HOH HOH . J 6 HOH A 135 449 144 HOH HOH . J 6 HOH A 136 450 145 HOH HOH . J 6 HOH A 137 451 146 HOH HOH . J 6 HOH A 138 452 147 HOH HOH . J 6 HOH A 139 453 148 HOH HOH . J 6 HOH A 140 454 149 HOH HOH . J 6 HOH A 141 455 150 HOH HOH . J 6 HOH A 142 456 151 HOH HOH . J 6 HOH A 143 457 152 HOH HOH . J 6 HOH A 144 458 153 HOH HOH . J 6 HOH A 145 459 154 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 O O5' CTN . . . C 3 24.629 25.328 32.137 1 50.59 ? O5' CTN 500 A 1 HETATM 2 C C5' CTN . . . C 3 23.296 25.438 31.63 1 53.85 ? C5' CTN 500 A 1 HETATM 3 C C4' CTN . . . C 3 23.215 26.498 30.56 1 56.8 ? C4' CTN 500 A 1 HETATM 4 O O4' CTN . . . C 3 22.161 26.19 29.609 1 56.02 ? O4' CTN 500 A 1 HETATM 5 C C1' CTN . . . C 3 21.611 27.409 29.175 1 57.95 ? C1' CTN 500 A 1 HETATM 6 N N1 CTN . . . C 3 20.289 27.166 28.532 1 58.81 ? N1 CTN 500 A 1 HETATM 7 C C6 CTN . . . C 3 20.327 26.968 27.166 1 58.21 ? C6 CTN 500 A 1 HETATM 8 C C5 CTN . . . C 3 19.244 26.741 26.419 1 58.04 ? C5 CTN 500 A 1 HETATM 9 C C4 CTN . . . C 3 18.009 26.714 27.124 1 60.66 ? C4 CTN 500 A 1 HETATM 10 N N3 CTN . . . C 3 17.938 26.905 28.455 1 58.98 ? N3 CTN 500 A 1 HETATM 11 C C2 CTN . . . C 3 19.058 27.136 29.186 1 59.08 ? C2 CTN 500 A 1 HETATM 12 O O2 CTN . . . C 3 19.009 27.316 30.405 1 62.24 ? O2 CTN 500 A 1 HETATM 13 N N4 CTN . . . C 3 16.879 26.493 26.443 1 61.43 ? N4 CTN 500 A 1 HETATM 14 C C2' CTN . . . C 3 21.603 28.296 30.41 1 60.26 ? C2' CTN 500 A 1 HETATM 15 O O2' CTN . . . C 3 21.46 29.667 30.068 1 62.6 ? O2' CTN 500 A 1 HETATM 16 C C3' CTN . . . C 3 22.961 27.934 31.043 1 56.69 ? C3' CTN 500 A 1 HETATM 17 O O3' CTN . . . C 3 23.97 28.787 30.512 1 54.02 ? O3' CTN 500 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #