data_9DA4 # _model_server_result.job_id urLwSzIO8fr-1L0WNg8QuQ _model_server_result.datetime_utc '2025-03-10 20:35:10' _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 9da4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 9DA4 # _exptl.entry_id 9DA4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 343.276 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{(3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-hydroxypyrrolidin-3-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 120 _cell.entry_id 9DA4 _cell.length_a 83.304 _cell.length_b 83.304 _cell.length_c 80.587 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DA4 _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 _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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -41.652 72.14338 13.431167 # _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 'C12 H18 N5 O5 P' _chem_comp.formula_weight 343.276 _chem_comp.id A1BBE _chem_comp.mon_nstd_flag . _chem_comp.name '{(3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-hydroxypyrrolidin-3-yl}methyl dihydrogen phosphate' _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 N6 C6 A1BBE sing 1 n n C6 N1 A1BBE doub 2 n y C6 C5 A1BBE sing 3 n y N7 C5 A1BBE sing 4 n y N7 C8 A1BBE sing 5 n y N1 C2 A1BBE sing 6 n y C5 C4 A1BBE doub 7 n y C8 C9 A1BBE doub 8 n y C2 N3 A1BBE doub 9 n y C4 C9 A1BBE sing 10 n y C4 N3 A1BBE sing 11 n y C9 C05 A1BBE sing 12 n n C05 N01 A1BBE sing 13 n n C12 N01 A1BBE sing 14 n n C12 C01 A1BBE sing 15 n n N01 C04 A1BBE sing 16 n n C04 C02 A1BBE sing 17 n n C01 C02 A1BBE sing 18 n n C01 O01 A1BBE sing 19 n n O05 P01 A1BBE doub 20 n n C02 C03 A1BBE sing 21 n n C03 O02 A1BBE sing 22 n n O02 P01 A1BBE sing 23 n n P01 O03 A1BBE sing 24 n n P01 O04 A1BBE sing 25 n n C2 H1 A1BBE sing 26 n n C01 H2 A1BBE sing 27 n n C02 H3 A1BBE sing 28 n n C03 H4 A1BBE sing 29 n n C03 H5 A1BBE sing 30 n n C04 H6 A1BBE sing 31 n n C04 H7 A1BBE sing 32 n n C05 H8 A1BBE sing 33 n n C05 H9 A1BBE sing 34 n n C12 H10 A1BBE sing 35 n n C12 H11 A1BBE sing 36 n n C8 H12 A1BBE sing 37 n n N6 H14 A1BBE sing 38 n n N6 H15 A1BBE sing 39 n n N7 H16 A1BBE sing 40 n n O01 H17 A1BBE sing 41 n n O03 H18 A1BBE sing 42 n n O04 H19 A1BBE sing 43 n n # _atom_sites.entry_id 9DA4 _atom_sites.fract_transf_matrix[1][1] 0.012004 _atom_sites.fract_transf_matrix[1][2] 0.006931 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013861 _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] 0.012409 _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 A1BBE A 1 201 201 A1BBE DIP . C 3 HOH A 1 301 50 HOH HOH . C 3 HOH A 2 302 33 HOH HOH . C 3 HOH A 3 303 13 HOH HOH . C 3 HOH A 4 304 24 HOH HOH . C 3 HOH A 5 305 26 HOH HOH . C 3 HOH A 6 306 25 HOH HOH . C 3 HOH A 7 307 23 HOH HOH . C 3 HOH A 8 308 77 HOH HOH . C 3 HOH A 9 309 64 HOH HOH . C 3 HOH A 10 310 48 HOH HOH . C 3 HOH A 11 311 11 HOH HOH . C 3 HOH A 12 312 34 HOH HOH . C 3 HOH A 13 313 15 HOH HOH . C 3 HOH A 14 314 76 HOH HOH . C 3 HOH A 15 315 66 HOH HOH . C 3 HOH A 16 316 44 HOH HOH . C 3 HOH A 17 317 19 HOH HOH . C 3 HOH A 18 318 45 HOH HOH . C 3 HOH A 19 319 56 HOH HOH . C 3 HOH A 20 320 4 HOH HOH . C 3 HOH A 21 321 51 HOH HOH . C 3 HOH A 22 322 65 HOH HOH . C 3 HOH A 23 323 2 HOH HOH . C 3 HOH A 24 324 37 HOH HOH . C 3 HOH A 25 325 71 HOH HOH . C 3 HOH A 26 326 75 HOH HOH . C 3 HOH A 27 327 3 HOH HOH . C 3 HOH A 28 328 62 HOH HOH . C 3 HOH A 29 329 55 HOH HOH . C 3 HOH A 30 330 12 HOH HOH . C 3 HOH A 31 331 43 HOH HOH . C 3 HOH A 32 332 20 HOH HOH . C 3 HOH A 33 333 63 HOH HOH . C 3 HOH A 34 334 18 HOH HOH . C 3 HOH A 35 335 52 HOH HOH . C 3 HOH A 36 336 42 HOH HOH . C 3 HOH A 37 337 41 HOH HOH . C 3 HOH A 38 338 5 HOH HOH . C 3 HOH A 39 339 1 HOH HOH . C 3 HOH A 40 340 46 HOH HOH . C 3 HOH A 41 341 9 HOH HOH . C 3 HOH A 42 342 10 HOH HOH . C 3 HOH A 43 343 22 HOH HOH . C 3 HOH A 44 344 72 HOH HOH . C 3 HOH A 45 345 30 HOH HOH . C 3 HOH A 46 346 6 HOH HOH . C 3 HOH A 47 347 54 HOH HOH . C 3 HOH A 48 348 31 HOH HOH . C 3 HOH A 49 349 61 HOH HOH . C 3 HOH A 50 350 59 HOH HOH . C 3 HOH A 51 351 49 HOH HOH . C 3 HOH A 52 352 14 HOH HOH . C 3 HOH A 53 353 8 HOH HOH . C 3 HOH A 54 354 47 HOH HOH . C 3 HOH A 55 355 21 HOH HOH . C 3 HOH A 56 356 74 HOH HOH . C 3 HOH A 57 357 68 HOH HOH . C 3 HOH A 58 358 36 HOH HOH . C 3 HOH A 59 359 57 HOH HOH . C 3 HOH A 60 360 16 HOH HOH . C 3 HOH A 61 361 38 HOH HOH . C 3 HOH A 62 362 27 HOH HOH . C 3 HOH A 63 363 69 HOH HOH . C 3 HOH A 64 364 7 HOH HOH . C 3 HOH A 65 365 35 HOH HOH . C 3 HOH A 66 366 40 HOH HOH . C 3 HOH A 67 367 28 HOH HOH . C 3 HOH A 68 368 17 HOH HOH . C 3 HOH A 69 369 39 HOH HOH . C 3 HOH A 70 370 78 HOH HOH . C 3 HOH A 71 371 29 HOH HOH . C 3 HOH A 72 372 53 HOH HOH . C 3 HOH A 73 373 58 HOH HOH . C 3 HOH A 74 374 67 HOH HOH . C 3 HOH A 75 375 70 HOH HOH . C 3 HOH A 76 376 32 HOH HOH . C 3 HOH A 77 377 73 HOH HOH . C 3 HOH A 78 378 60 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 C C2 A1BBE . . . B 2 -16.512 39.075 -6.381 1 28.5 ? C2 A1BBE 201 A 1 HETATM 2 C C4 A1BBE . . . B 2 -16.773 36.79 -6.176 1 26.49 ? C4 A1BBE 201 A 1 HETATM 3 C C5 A1BBE . . . B 2 -16.046 36.602 -7.34 1 25.44 ? C5 A1BBE 201 A 1 HETATM 4 C C01 A1BBE . . . B 2 -15.284 34.443 -2.085 1 22.67 ? C01 A1BBE 201 A 1 HETATM 5 C C02 A1BBE . . . B 2 -15.876 35.443 -1.502 1 23.96 ? C02 A1BBE 201 A 1 HETATM 6 C C03 A1BBE . . . B 2 -14.868 36.564 -1 1 26.4 ? C03 A1BBE 201 A 1 HETATM 7 C C04 A1BBE . . . B 2 -16.849 36.102 -2.643 1 24.16 ? C04 A1BBE 201 A 1 HETATM 8 C C05 A1BBE . . . B 2 -18.008 35.103 -4.525 1 25.2 ? C05 A1BBE 201 A 1 HETATM 9 C C12 A1BBE . . . B 2 -16.253 34.028 -3.39 1 22.5 ? C12 A1BBE 201 A 1 HETATM 10 C C6 A1BBE . . . B 2 -15.529 37.736 -7.993 1 26.22 ? C6 A1BBE 201 A 1 HETATM 11 C C8 A1BBE . . . B 2 -16.595 34.606 -6.671 1 26.23 ? C8 A1BBE 201 A 1 HETATM 12 C C9 A1BBE . . . B 2 -17.121 35.49 -5.727 1 23.26 ? C9 A1BBE 201 A 1 HETATM 13 N N01 A1BBE . . . B 2 -17.34 34.813 -3.263 1 21.92 ? N01 A1BBE 201 A 1 HETATM 14 N N1 A1BBE . . . B 2 -15.81 38.931 -7.508 1 28.03 ? N1 A1BBE 201 A 1 HETATM 15 N N3 A1BBE . . . B 2 -16.993 38.032 -5.713 1 25.72 ? N3 A1BBE 201 A 1 HETATM 16 N N6 A1BBE . . . B 2 -14.765 37.593 -9.221 1 27.73 ? N6 A1BBE 201 A 1 HETATM 17 N N7 A1BBE . . . B 2 -15.949 35.292 -7.602 1 24.99 ? N7 A1BBE 201 A 1 HETATM 18 O O01 A1BBE . . . B 2 -15.226 33.274 -1.222 1 22.39 ? O01 A1BBE 201 A 1 HETATM 19 O O02 A1BBE . . . B 2 -15.648 37.605 -0.44 1 23.38 ? O02 A1BBE 201 A 1 HETATM 20 O O03 A1BBE . . . B 2 -13.638 39.027 0.196 1 23.36 -1 O03 A1BBE 201 A 1 HETATM 21 O O04 A1BBE . . . B 2 -15.945 39.992 0.397 1 23.8 -1 O04 A1BBE 201 A 1 HETATM 22 O O05 A1BBE . . . B 2 -14.928 39.585 -1.865 1 24.43 ? O05 A1BBE 201 A 1 HETATM 23 P P01 A1BBE . . . B 2 -15.018 39.133 -0.423 1 22.89 ? P01 A1BBE 201 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #