data_2NSH # _model_server_result.job_id iLf51gNiwOxljP3B2DkkcA _model_server_result.datetime_utc '2024-11-16 12:56:19' _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 2nsh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 2NSH # _exptl.entry_id 2NSH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.184 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' _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 2NSH _cell.length_a 111.688 _cell.length_b 111.688 _cell.length_c 49.412 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NSH _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 0 0 -49.412 6 'crystal symmetry operation' 6_554 x,-y,-z-1 1 0 0 0 -1 0 0 0 -1 0 0 -49.412 7 'crystal symmetry operation' 7_554 y,x,-z-1 0 1 0 1 0 0 0 0 -1 0 0 -49.412 8 'crystal symmetry operation' 8_554 -y,-x,-z-1 0 -1 0 -1 0 0 0 0 -1 0 0 -49.412 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C8 H13 N4 O9 P' _chem_comp.formula_weight 340.184 _chem_comp.id NIA _chem_comp.mon_nstd_flag . _chem_comp.name '((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '4-NITRO-5-AMINOIMIDAZOLE RIBONUCLEOTIDE;NITRO AIR' # 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 O8 P NIA sing 224 n n O8 HO8 NIA sing 225 n n P O6 NIA doub 226 n n P O7 NIA sing 227 n n P O5' NIA sing 228 n n O7 HO7 NIA sing 229 n n O5' C5' NIA sing 230 n n C5' C4' NIA sing 231 n n C5' "H5'1" NIA sing 232 n n C5' "H5'2" NIA sing 233 n n C4' C3' NIA sing 234 n n C4' O4' NIA sing 235 n n C4' H4' NIA sing 236 n n C3' O3' NIA sing 237 n n C3' C2' NIA sing 238 n n C3' H3' NIA sing 239 n n O3' H1 NIA sing 240 n n C2' O2' NIA sing 241 n n C2' C1' NIA sing 242 n n C2' H2' NIA sing 243 n n O2' H2 NIA sing 244 n n O4' C1' NIA sing 245 n n C1' N1 NIA sing 246 n n C1' H1' NIA sing 247 n n N1 C5 NIA sing 248 n y N1 C2 NIA sing 249 n y C5 N6 NIA sing 250 n n C5 C4 NIA doub 251 n y N6 HN61 NIA sing 252 n n N6 HN62 NIA sing 253 n n C4 N7 NIA sing 254 n n C4 N3 NIA sing 255 n y N7 O72 NIA doub 256 n n N7 O71 NIA sing 257 n n N3 C2 NIA doub 258 n y C2 H3 NIA sing 259 n n # _atom_sites.entry_id 2NSH _atom_sites.fract_transf_matrix[1][1] 0.008954 _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] 0.008954 _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] 0.020238 _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 NIA A 1 300 300 NIA NIA . C 3 HOH A 1 301 5 HOH HOH . C 3 HOH A 2 302 6 HOH HOH . C 3 HOH A 3 303 7 HOH HOH . C 3 HOH A 4 304 8 HOH HOH . C 3 HOH A 5 305 10 HOH HOH . C 3 HOH A 6 306 12 HOH HOH . C 3 HOH A 7 307 13 HOH HOH . C 3 HOH A 8 308 14 HOH HOH . C 3 HOH A 9 309 16 HOH HOH . C 3 HOH A 10 310 17 HOH HOH . C 3 HOH A 11 311 18 HOH HOH . C 3 HOH A 12 312 19 HOH HOH . C 3 HOH A 13 313 20 HOH HOH . C 3 HOH A 14 314 24 HOH HOH . C 3 HOH A 15 315 29 HOH HOH . C 3 HOH A 16 316 30 HOH HOH . C 3 HOH A 17 317 32 HOH HOH . C 3 HOH A 18 318 34 HOH HOH . C 3 HOH A 19 319 36 HOH HOH . C 3 HOH A 20 320 38 HOH HOH . C 3 HOH A 21 321 40 HOH HOH . C 3 HOH A 22 322 41 HOH HOH . C 3 HOH A 23 323 45 HOH HOH . C 3 HOH A 24 324 46 HOH HOH . C 3 HOH A 25 325 48 HOH HOH . C 3 HOH A 26 326 51 HOH HOH . C 3 HOH A 27 327 52 HOH HOH . C 3 HOH A 28 328 54 HOH HOH . C 3 HOH A 29 329 57 HOH HOH . C 3 HOH A 30 330 58 HOH HOH . C 3 HOH A 31 331 59 HOH HOH . C 3 HOH A 32 332 60 HOH HOH . C 3 HOH A 33 333 63 HOH HOH . C 3 HOH A 34 334 67 HOH HOH . C 3 HOH A 35 335 68 HOH HOH . C 3 HOH A 36 336 71 HOH HOH . C 3 HOH A 37 337 72 HOH HOH . C 3 HOH A 38 338 73 HOH HOH . C 3 HOH A 39 339 74 HOH HOH . C 3 HOH A 40 340 75 HOH HOH . C 3 HOH A 41 341 77 HOH HOH . C 3 HOH A 42 342 78 HOH HOH . C 3 HOH A 43 343 79 HOH HOH . C 3 HOH A 44 344 81 HOH HOH . C 3 HOH A 45 345 83 HOH HOH . C 3 HOH A 46 346 84 HOH HOH . C 3 HOH A 47 347 87 HOH HOH . C 3 HOH A 48 348 89 HOH HOH . C 3 HOH A 49 349 90 HOH HOH . C 3 HOH A 50 350 91 HOH HOH . C 3 HOH A 51 351 92 HOH HOH . C 3 HOH A 52 352 94 HOH HOH . C 3 HOH A 53 353 95 HOH HOH . C 3 HOH A 54 354 96 HOH HOH . C 3 HOH A 55 355 101 HOH HOH . C 3 HOH A 56 356 102 HOH HOH . C 3 HOH A 57 357 103 HOH HOH . C 3 HOH A 58 358 104 HOH HOH . C 3 HOH A 59 359 105 HOH HOH . C 3 HOH A 60 360 106 HOH HOH . C 3 HOH A 61 361 108 HOH HOH . C 3 HOH A 62 362 111 HOH HOH . C 3 HOH A 63 363 112 HOH HOH . C 3 HOH A 64 364 113 HOH HOH . C 3 HOH A 65 365 114 HOH HOH . C 3 HOH A 66 366 115 HOH HOH . C 3 HOH A 67 367 116 HOH HOH . C 3 HOH A 68 368 117 HOH HOH . C 3 HOH A 69 369 119 HOH HOH . C 3 HOH A 70 370 120 HOH HOH . C 3 HOH A 71 371 121 HOH HOH . C 3 HOH A 72 372 122 HOH HOH . C 3 HOH A 73 373 123 HOH HOH . C 3 HOH A 74 374 124 HOH HOH . C 3 HOH A 75 375 125 HOH HOH . C 3 HOH A 76 376 126 HOH HOH . C 3 HOH A 77 377 127 HOH HOH . C 3 HOH A 78 378 128 HOH HOH . C 3 HOH A 79 379 129 HOH HOH . C 3 HOH A 80 380 130 HOH HOH . C 3 HOH A 81 381 131 HOH HOH . C 3 HOH A 82 382 132 HOH HOH . C 3 HOH A 83 383 133 HOH HOH . C 3 HOH A 84 384 134 HOH HOH . C 3 HOH A 85 385 135 HOH HOH . C 3 HOH A 86 386 136 HOH HOH . C 3 HOH A 87 387 137 HOH HOH . C 3 HOH A 88 388 138 HOH HOH . C 3 HOH A 89 389 139 HOH HOH . C 3 HOH A 90 390 140 HOH HOH . C 3 HOH A 91 391 141 HOH HOH . C 3 HOH A 92 392 142 HOH HOH . C 3 HOH A 93 393 143 HOH HOH . C 3 HOH A 94 394 144 HOH HOH . C 3 HOH A 95 395 145 HOH HOH . C 3 HOH A 96 396 146 HOH HOH . C 3 HOH A 97 397 147 HOH HOH . C 3 HOH A 98 398 148 HOH HOH . C 3 HOH A 99 399 149 HOH HOH . C 3 HOH A 100 400 150 HOH HOH . C 3 HOH A 101 401 151 HOH HOH . C 3 HOH A 102 402 152 HOH HOH . C 3 HOH A 103 403 153 HOH HOH . C 3 HOH A 104 404 154 HOH HOH . C 3 HOH A 105 405 155 HOH HOH . C 3 HOH A 106 406 156 HOH HOH . C 3 HOH A 107 407 157 HOH HOH . C 3 HOH A 108 408 158 HOH HOH . C 3 HOH A 109 409 159 HOH HOH . C 3 HOH A 110 410 160 HOH HOH . C 3 HOH A 111 411 161 HOH HOH . C 3 HOH A 112 412 162 HOH HOH . C 3 HOH A 113 413 163 HOH HOH . C 3 HOH A 114 414 164 HOH HOH . C 3 HOH A 115 415 165 HOH HOH . C 3 HOH A 116 416 166 HOH HOH . C 3 HOH A 117 417 167 HOH HOH . C 3 HOH A 118 418 168 HOH HOH . C 3 HOH A 119 419 169 HOH HOH . C 3 HOH A 120 420 170 HOH HOH . C 3 HOH A 121 421 171 HOH HOH . C 3 HOH A 122 422 172 HOH HOH . C 3 HOH A 123 423 173 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 O8 NIA . . . B 2 16.594 -10.562 -9.897 1 40.24 ? O8 NIA 300 A 1 HETATM 2 P P NIA . . . B 2 15.677 -11.861 -9.543 1 42.88 ? P NIA 300 A 1 HETATM 3 O O6 NIA . . . B 2 14.57 -11.446 -8.414 1 44.68 ? O6 NIA 300 A 1 HETATM 4 O O7 NIA . . . B 2 16.49 -13.048 -9.147 1 41.88 ? O7 NIA 300 A 1 HETATM 5 O O5' NIA . . . B 2 14.901 -12.211 -10.912 1 39.67 ? O5' NIA 300 A 1 HETATM 6 C C5' NIA . . . B 2 14.007 -11.285 -11.479 1 36.8 ? C5' NIA 300 A 1 HETATM 7 C C4' NIA . . . B 2 13.471 -11.876 -12.726 1 35.96 ? C4' NIA 300 A 1 HETATM 8 C C3' NIA . . . B 2 12.695 -13.139 -12.308 1 35.57 ? C3' NIA 300 A 1 HETATM 9 O O3' NIA . . . B 2 11.327 -12.989 -12.668 1 34.87 ? O3' NIA 300 A 1 HETATM 10 C C2' NIA . . . B 2 13.339 -14.226 -13.173 1 34.96 ? C2' NIA 300 A 1 HETATM 11 O O2' NIA . . . B 2 12.356 -15.109 -13.777 1 31.64 ? O2' NIA 300 A 1 HETATM 12 O O4' NIA . . . B 2 14.668 -12.363 -13.431 1 36.35 ? O4' NIA 300 A 1 HETATM 13 C C1' NIA . . . B 2 14.084 -13.379 -14.227 1 35.97 ? C1' NIA 300 A 1 HETATM 14 N N1 NIA . . . B 2 14.912 -14.341 -14.909 1 35.97 ? N1 NIA 300 A 1 HETATM 15 C C5 NIA . . . B 2 14.69 -14.65 -16.171 1 36.87 ? C5 NIA 300 A 1 HETATM 16 N N6 NIA . . . B 2 13.769 -14.083 -16.989 1 35.75 ? N6 NIA 300 A 1 HETATM 17 C C4 NIA . . . B 2 15.608 -15.616 -16.481 1 37.69 ? C4 NIA 300 A 1 HETATM 18 N N7 NIA . . . B 2 15.613 -16.166 -17.672 1 40.11 ? N7 NIA 300 A 1 HETATM 19 O O72 NIA . . . B 2 14.597 -15.791 -18.641 1 37.77 ? O72 NIA 300 A 1 HETATM 20 O O71 NIA . . . B 2 16.51 -17.166 -17.932 1 41.8 ? O71 NIA 300 A 1 HETATM 21 N N3 NIA . . . B 2 16.37 -15.91 -15.409 1 35.38 ? N3 NIA 300 A 1 HETATM 22 C C2 NIA . . . B 2 15.916 -15.117 -14.436 1 36.6 ? C2 NIA 300 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 22 #