data_3BGS # _model_server_result.job_id QEShoqSm0iMTvT77X7_u6A _model_server_result.datetime_utc '2024-11-25 20:41:40' _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 3bgs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 3BGS # _exptl.entry_id 3BGS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 265.288 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one _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 3BGS _cell.length_a 142.801 _cell.length_b 142.801 _cell.length_c 167.348 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BGS _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H17 N4 O3 1' _chem_comp.formula_weight 265.288 _chem_comp.id DIH _chem_comp.mon_nstd_flag . _chem_comp.name 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one _chem_comp.type non-polymer _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 O6 C6 DIH doub 83 n n C6 N1 DIH sing 84 n n C6 C5 DIH sing 85 n n N7 C5 DIH sing 86 n y N7 C8 DIH sing 87 n y N1 C2 DIH sing 88 n n C5 C4 DIH doub 89 n y C8 C9 DIH doub 90 n y C2 N3 DIH doub 91 n n C4 C9 DIH sing 92 n y C4 N3 DIH sing 93 n n C9 C10 DIH sing 94 n n C10 N1' DIH sing 95 n n N1' C6' DIH sing 96 n n N1' C2' DIH sing 97 n n C6' C4' DIH sing 98 n n C2' C3' DIH sing 99 n n O5' C5' DIH sing 100 n n C5' C4' DIH sing 101 n n C4' C3' DIH sing 102 n n C3' O3' DIH sing 103 n n O5' H1 DIH sing 104 n n C5' H2 DIH sing 105 n n C5' H3 DIH sing 106 n n C4' H4 DIH sing 107 n n C6' H5 DIH sing 108 n n C6' H6 DIH sing 109 n n C3' H7 DIH sing 110 n n O3' H8 DIH sing 111 n n C2' H9 DIH sing 112 n n C2' H10 DIH sing 113 n n N1' H11 DIH sing 114 n n C10 H12 DIH sing 115 n n C10 H13 DIH sing 116 n n C8 H14 DIH sing 117 n n N7 H15 DIH sing 118 n n N1 H16 DIH sing 119 n n C2 H17 DIH sing 120 n n # _atom_sites.entry_id 3BGS _atom_sites.fract_transf_matrix[1][1] 0.007003 _atom_sites.fract_transf_matrix[1][2] 0.004043 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008086 _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] 0.005976 _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 1 302 302 PO4 PO4 . C 2 PO4 A 1 303 303 PO4 PO4 . D 2 PO4 A 1 304 304 PO4 PO4 . E 3 DIH A 1 301 301 DIH DIH . F 4 HOH A 1 305 4 HOH HOH . F 4 HOH A 2 306 6 HOH HOH . F 4 HOH A 3 307 7 HOH HOH . F 4 HOH A 4 308 9 HOH HOH . F 4 HOH A 5 309 11 HOH HOH . F 4 HOH A 6 310 13 HOH HOH . F 4 HOH A 7 311 14 HOH HOH . F 4 HOH A 8 312 15 HOH HOH . F 4 HOH A 9 313 16 HOH HOH . F 4 HOH A 10 314 17 HOH HOH . F 4 HOH A 11 315 19 HOH HOH . F 4 HOH A 12 316 21 HOH HOH . F 4 HOH A 13 317 22 HOH HOH . F 4 HOH A 14 318 23 HOH HOH . F 4 HOH A 15 319 24 HOH HOH . F 4 HOH A 16 320 25 HOH HOH . F 4 HOH A 17 321 26 HOH HOH . F 4 HOH A 18 322 28 HOH HOH . F 4 HOH A 19 323 31 HOH HOH . F 4 HOH A 20 324 32 HOH HOH . F 4 HOH A 21 325 34 HOH HOH . F 4 HOH A 22 326 35 HOH HOH . F 4 HOH A 23 327 36 HOH HOH . F 4 HOH A 24 328 39 HOH HOH . F 4 HOH A 25 329 41 HOH HOH . F 4 HOH A 26 330 42 HOH HOH . F 4 HOH A 27 331 43 HOH HOH . F 4 HOH A 28 332 47 HOH HOH . F 4 HOH A 29 333 48 HOH HOH . F 4 HOH A 30 334 51 HOH HOH . F 4 HOH A 31 335 54 HOH HOH . F 4 HOH A 32 336 56 HOH HOH . F 4 HOH A 33 337 57 HOH HOH . F 4 HOH A 34 338 59 HOH HOH . F 4 HOH A 35 339 60 HOH HOH . F 4 HOH A 36 340 62 HOH HOH . F 4 HOH A 37 341 64 HOH HOH . F 4 HOH A 38 342 67 HOH HOH . F 4 HOH A 39 343 68 HOH HOH . F 4 HOH A 40 344 69 HOH HOH . F 4 HOH A 41 345 71 HOH HOH . F 4 HOH A 42 346 81 HOH HOH . F 4 HOH A 43 347 87 HOH HOH . F 4 HOH A 44 348 93 HOH HOH . F 4 HOH A 45 349 94 HOH HOH . F 4 HOH A 46 350 96 HOH HOH . F 4 HOH A 47 351 98 HOH HOH . F 4 HOH A 48 352 103 HOH HOH . F 4 HOH A 49 353 104 HOH HOH . F 4 HOH A 50 354 107 HOH HOH . F 4 HOH A 51 355 112 HOH HOH . F 4 HOH A 52 356 113 HOH HOH . F 4 HOH A 53 357 115 HOH HOH . F 4 HOH A 54 358 120 HOH HOH . F 4 HOH A 55 359 133 HOH HOH . F 4 HOH A 56 360 139 HOH HOH . F 4 HOH A 57 361 140 HOH HOH . F 4 HOH A 58 362 141 HOH HOH . F 4 HOH A 59 363 142 HOH HOH . F 4 HOH A 60 364 143 HOH HOH . F 4 HOH A 61 365 154 HOH HOH . F 4 HOH A 62 366 163 HOH HOH . F 4 HOH A 63 367 168 HOH HOH . F 4 HOH A 64 368 172 HOH HOH . F 4 HOH A 65 369 173 HOH HOH . F 4 HOH A 66 370 174 HOH HOH . F 4 HOH A 67 371 175 HOH HOH . F 4 HOH A 68 372 176 HOH HOH . F 4 HOH A 69 373 177 HOH HOH . F 4 HOH A 70 374 178 HOH HOH . F 4 HOH A 71 375 179 HOH HOH . F 4 HOH A 72 376 180 HOH HOH . F 4 HOH A 73 377 182 HOH HOH . F 4 HOH A 74 378 183 HOH HOH . F 4 HOH A 75 379 184 HOH HOH . F 4 HOH A 76 380 185 HOH HOH . F 4 HOH A 77 381 186 HOH HOH . F 4 HOH A 78 382 187 HOH HOH . F 4 HOH A 79 383 188 HOH HOH . F 4 HOH A 80 384 189 HOH HOH . F 4 HOH A 81 385 190 HOH HOH . F 4 HOH A 82 386 191 HOH HOH . F 4 HOH A 83 387 192 HOH HOH . F 4 HOH A 84 388 193 HOH HOH . F 4 HOH A 85 389 194 HOH HOH . F 4 HOH A 86 390 195 HOH HOH . F 4 HOH A 87 391 196 HOH HOH . F 4 HOH A 88 392 197 HOH HOH . F 4 HOH A 89 393 199 HOH HOH . F 4 HOH A 90 394 202 HOH HOH . F 4 HOH A 91 395 203 HOH HOH . F 4 HOH A 92 396 204 HOH HOH . F 4 HOH A 93 397 206 HOH HOH . F 4 HOH A 94 398 208 HOH HOH . F 4 HOH A 95 399 209 HOH HOH . F 4 HOH A 96 400 210 HOH HOH . F 4 HOH A 97 401 211 HOH HOH . F 4 HOH A 98 402 212 HOH HOH . F 4 HOH A 99 403 213 HOH HOH . F 4 HOH A 100 404 215 HOH HOH . F 4 HOH A 101 405 217 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' DIH . . . E 3 17.494 12.134 59.898 1 65.21 ? O5' DIH 301 A 1 HETATM 2 C C5' DIH . . . E 3 16.732 10.96 60.165 1 61.09 ? C5' DIH 301 A 1 HETATM 3 C C4' DIH . . . E 3 15.35 11.337 60.703 1 60.34 ? C4' DIH 301 A 1 HETATM 4 C C6' DIH . . . E 3 14.405 11.314 59.527 1 58 ? C6' DIH 301 A 1 HETATM 5 C C3' DIH . . . E 3 15.21 12.753 61.26 1 62.98 ? C3' DIH 301 A 1 HETATM 6 O O3' DIH . . . E 3 14.198 12.687 62.313 1 62.57 ? O3' DIH 301 A 1 HETATM 7 C C2' DIH . . . E 3 14.743 13.614 60.063 1 62.79 ? C2' DIH 301 A 1 HETATM 8 N N1' DIH . . . E 3 14.625 12.659 58.929 1 57.81 ? N1' DIH 301 A 1 HETATM 9 C C10 DIH . . . E 3 13.64 12.917 57.849 1 48.46 ? C10 DIH 301 A 1 HETATM 10 C C9 DIH . . . E 3 14.251 12.15 56.68 1 43.32 ? C9 DIH 301 A 1 HETATM 11 C C8 DIH . . . E 3 15.314 12.568 55.872 1 42.97 ? C8 DIH 301 A 1 HETATM 12 N N7 DIH . . . E 3 15.606 11.606 54.958 1 44.66 ? N7 DIH 301 A 1 HETATM 13 C C5 DIH . . . E 3 14.767 10.526 55.112 1 45.24 ? C5 DIH 301 A 1 HETATM 14 C C6 DIH . . . E 3 14.594 9.285 54.494 1 46.64 ? C6 DIH 301 A 1 HETATM 15 O O6 DIH . . . E 3 15.331 8.911 53.541 1 46.03 ? O6 DIH 301 A 1 HETATM 16 N N1 DIH . . . E 3 13.619 8.436 54.96 1 44.73 ? N1 DIH 301 A 1 HETATM 17 C C2 DIH . . . E 3 12.82 8.781 55.987 1 42.7 ? C2 DIH 301 A 1 HETATM 18 N N3 DIH . . . E 3 12.958 9.932 56.618 1 44.32 ? N3 DIH 301 A 1 HETATM 19 C C4 DIH . . . E 3 13.92 10.804 56.178 1 45.17 ? C4 DIH 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #