data_5X3D # _model_server_result.job_id 8PUfsjE4U_YNz62PBqu_dQ _model_server_result.datetime_utc '2025-04-03 23:21:00' _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 5x3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5X3D # _exptl.entry_id 5X3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 431.23 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid' _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 5X3D _cell.length_a 71.909 _cell.length_b 71.909 _cell.length_c 109.507 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 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' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 35.9545 62.275021 18.251167 # _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 'C11 H19 N3 O11 P2' _chem_comp.formula_weight 431.23 _chem_comp.id 7XL _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-(2-hydroxyethyl)phosphinic acid' _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 C11 C10 7XL sing 1 n n C11 O11 7XL sing 2 n n C10 P2 7XL sing 3 n n O9 P2 7XL doub 4 n n P2 O8 7XL sing 5 n n P2 O10 7XL sing 6 n n O8 P1 7XL sing 7 n n O6 P1 7XL doub 8 n n P1 O7 7XL sing 9 n n P1 O5 7XL sing 10 n n C9 O5 7XL sing 11 n n C9 C8 7XL sing 12 n n C8 C7 7XL sing 13 n n C8 O2 7XL sing 14 n n C7 O4 7XL sing 15 n n C7 C6 7XL sing 16 n n O2 C5 7XL sing 17 n n C6 O3 7XL sing 18 n n C6 C5 7XL sing 19 n n C5 N3 7XL sing 20 n n C4 N3 7XL sing 21 n n C4 C3 7XL doub 22 n n N3 C1 7XL sing 23 n n C3 C2 7XL sing 24 n n C1 O1 7XL doub 25 n n C1 N1 7XL sing 26 n n C2 N1 7XL doub 27 n n C2 N2 7XL sing 28 n n N2 H1 7XL sing 29 n n N2 H2 7XL sing 30 n n C3 H3 7XL sing 31 n n C4 H4 7XL sing 32 n n C5 H5 7XL sing 33 n n C6 H6 7XL sing 34 n n O3 H7 7XL sing 35 n n C7 H8 7XL sing 36 n n O4 H9 7XL sing 37 n n C8 H10 7XL sing 38 n n C9 H11 7XL sing 39 n n C9 H12 7XL sing 40 n n O7 H13 7XL sing 41 n n O10 H14 7XL sing 42 n n C10 H15 7XL sing 43 n n C10 H16 7XL sing 44 n n C11 H17 7XL sing 45 n n C11 H18 7XL sing 46 n n O11 H19 7XL sing 47 n n # _atom_sites.entry_id 5X3D _atom_sites.fract_transf_matrix[1][1] 0.013906 _atom_sites.fract_transf_matrix[1][2] 0.008029 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016058 _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] 0.009132 _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 7XL A 1 201 1 7XL DRG . C 3 HOH A 1 301 35 HOH HOH . C 3 HOH A 2 302 46 HOH HOH . C 3 HOH A 3 303 33 HOH HOH . C 3 HOH A 4 304 56 HOH HOH . C 3 HOH A 5 305 63 HOH HOH . C 3 HOH A 6 306 61 HOH HOH . C 3 HOH A 7 307 27 HOH HOH . C 3 HOH A 8 308 64 HOH HOH . C 3 HOH A 9 309 37 HOH HOH . C 3 HOH A 10 310 62 HOH HOH . C 3 HOH A 11 311 17 HOH HOH . C 3 HOH A 12 312 65 HOH HOH . C 3 HOH A 13 313 6 HOH HOH . C 3 HOH A 14 314 34 HOH HOH . C 3 HOH A 15 315 15 HOH HOH . C 3 HOH A 16 316 54 HOH HOH . C 3 HOH A 17 317 13 HOH HOH . C 3 HOH A 18 318 20 HOH HOH . C 3 HOH A 19 319 52 HOH HOH . C 3 HOH A 20 320 74 HOH HOH . C 3 HOH A 21 321 58 HOH HOH . C 3 HOH A 22 322 10 HOH HOH . C 3 HOH A 23 323 19 HOH HOH . C 3 HOH A 24 324 24 HOH HOH . C 3 HOH A 25 325 57 HOH HOH . C 3 HOH A 26 326 26 HOH HOH . C 3 HOH A 27 327 30 HOH HOH . C 3 HOH A 28 328 49 HOH HOH . C 3 HOH A 29 329 25 HOH HOH . C 3 HOH A 30 330 72 HOH HOH . C 3 HOH A 31 331 16 HOH HOH . C 3 HOH A 32 332 9 HOH HOH . C 3 HOH A 33 333 66 HOH HOH . C 3 HOH A 34 334 36 HOH HOH . C 3 HOH A 35 335 38 HOH HOH . C 3 HOH A 36 336 75 HOH HOH . C 3 HOH A 37 337 7 HOH HOH . C 3 HOH A 38 338 29 HOH HOH . C 3 HOH A 39 339 73 HOH HOH . C 3 HOH A 40 340 11 HOH HOH . C 3 HOH A 41 341 60 HOH HOH . C 3 HOH A 42 342 12 HOH HOH . C 3 HOH A 43 343 76 HOH HOH . C 3 HOH A 44 344 55 HOH HOH . C 3 HOH A 45 345 67 HOH HOH . C 3 HOH A 46 346 51 HOH HOH . C 3 HOH A 47 347 43 HOH HOH . C 3 HOH A 48 348 1 HOH HOH . C 3 HOH A 49 349 59 HOH HOH . C 3 HOH A 50 350 14 HOH HOH . C 3 HOH A 51 351 4 HOH HOH . C 3 HOH A 52 352 22 HOH HOH . C 3 HOH A 53 353 23 HOH HOH . C 3 HOH A 54 354 21 HOH HOH . C 3 HOH A 55 355 5 HOH HOH . C 3 HOH A 56 356 45 HOH HOH . C 3 HOH A 57 357 32 HOH HOH . C 3 HOH A 58 358 31 HOH HOH . C 3 HOH A 59 359 18 HOH HOH . C 3 HOH A 60 360 53 HOH HOH . C 3 HOH A 61 361 8 HOH HOH . C 3 HOH A 62 362 69 HOH HOH . C 3 HOH A 63 363 71 HOH HOH . C 3 HOH A 64 364 2 HOH HOH . C 3 HOH A 65 365 3 HOH HOH . C 3 HOH A 66 366 70 HOH HOH . C 3 HOH A 67 367 47 HOH HOH . C 3 HOH A 68 368 68 HOH HOH . C 3 HOH A 69 369 28 HOH HOH . C 3 HOH A 70 370 44 HOH HOH . C 3 HOH A 71 371 48 HOH HOH . C 3 HOH A 72 372 40 HOH HOH . C 3 HOH A 73 373 50 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 O1 7XL . . . B 2 0.241 25.933 14.55 1 25.7 ? O1 7XL 201 A 1 HETATM 2 C C1 7XL . . . B 2 -0.23 26.991 14.105 1 30.39 ? C1 7XL 201 A 1 HETATM 3 N N1 7XL . . . B 2 -0.688 27.912 14.974 1 30.88 ? N1 7XL 201 A 1 HETATM 4 C C2 7XL . . . B 2 -1.25 29.069 14.563 1 35.06 ? C2 7XL 201 A 1 HETATM 5 N N2 7XL . . . B 2 -1.685 29.94 15.48 1 35.6 ? N2 7XL 201 A 1 HETATM 6 C C3 7XL . . . B 2 -1.373 29.363 13.188 1 33.4 ? C3 7XL 201 A 1 HETATM 7 C C4 7XL . . . B 2 -0.884 28.434 12.271 1 30.85 ? C4 7XL 201 A 1 HETATM 8 N N3 7XL . . . B 2 -0.322 27.224 12.757 1 28.99 ? N3 7XL 201 A 1 HETATM 9 C C5 7XL . . . B 2 0.197 26.194 11.831 1 26.03 ? C5 7XL 201 A 1 HETATM 10 O O2 7XL . . . B 2 1.08 26.839 10.928 1 26.35 ? O2 7XL 201 A 1 HETATM 11 C C6 7XL . . . B 2 -0.835 25.595 10.95 1 25.46 ? C6 7XL 201 A 1 HETATM 12 O O3 7XL . . . B 2 -1.501 24.517 11.638 1 26.9 ? O3 7XL 201 A 1 HETATM 13 C C7 7XL . . . B 2 0.002 25.083 9.788 1 25.01 ? C7 7XL 201 A 1 HETATM 14 O O4 7XL . . . B 2 0.545 23.778 10.042 1 25.26 ? O4 7XL 201 A 1 HETATM 15 C C8 7XL . . . B 2 1.171 26.082 9.705 1 26.11 ? C8 7XL 201 A 1 HETATM 16 C C9 7XL . . . B 2 1.026 27.075 8.562 1 26.39 ? C9 7XL 201 A 1 HETATM 17 O O5 7XL . . . B 2 -0.267 27.649 8.662 1 28.8 ? O5 7XL 201 A 1 HETATM 18 P P1 7XL . . . B 2 -0.956 28.319 7.303 1 30.49 ? P1 7XL 201 A 1 HETATM 19 O O6 7XL . . . B 2 0.174 29.239 6.726 1 29 ? O6 7XL 201 A 1 HETATM 20 O O7 7XL . . . B 2 -2.236 28.876 7.719 1 30.14 ? O7 7XL 201 A 1 HETATM 21 O O8 7XL . . . B 2 -1.042 27.046 6.323 1 29.26 ? O8 7XL 201 A 1 HETATM 22 P P2 7XL . . . B 2 -2.319 26.102 5.927 1 29.58 ? P2 7XL 201 A 1 HETATM 23 O O9 7XL . . . B 2 -3.504 27.049 5.385 1 32.47 ? O9 7XL 201 A 1 HETATM 24 O O10 7XL . . . B 2 -2.787 25.215 7.022 1 29.56 ? O10 7XL 201 A 1 HETATM 25 C C10 7XL . . . B 2 -1.494 25.202 4.574 1 26.17 ? C10 7XL 201 A 1 HETATM 26 C C11 7XL . . . B 2 -2.32 24.1 3.99 1 26.86 ? C11 7XL 201 A 1 HETATM 27 O O11 7XL . . . B 2 -2.4 23.002 4.929 1 25.72 ? O11 7XL 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #