data_3X0K # _model_server_result.job_id e0tIdDepHzU9oodZfoMm6g _model_server_result.datetime_utc '2024-10-19 03:54:43' _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 3x0k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 3X0K # _exptl.entry_id 3X0K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN 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 3X0K _cell.length_a 49.645 _cell.length_b 49.645 _cell.length_c 118.673 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3X0K _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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' 4_555 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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id AR6 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose # 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 N1 C2 AR6 doub 13 n y N1 C6 AR6 sing 14 n y C2 N3 AR6 sing 15 n y N3 C4 AR6 doub 16 n y C4 C5 AR6 sing 17 n y C4 N9 AR6 sing 18 n y C5 C6 AR6 doub 19 n y C5 N7 AR6 sing 20 n y C6 N6 AR6 sing 21 n n N7 C8 AR6 doub 22 n y C8 N9 AR6 sing 23 n y N9 C1' AR6 sing 24 n n PA O1A AR6 sing 25 n n PA O2A AR6 doub 26 n n PA O3A AR6 sing 27 n n PA O5' AR6 sing 28 n n PB O1B AR6 sing 29 n n PB O2B AR6 doub 30 n n PB O3A AR6 sing 31 n n PB O5D AR6 sing 32 n n C1' C2' AR6 sing 33 n n C1' O4' AR6 sing 34 n n C1D O1D AR6 sing 35 n n C1D C2D AR6 sing 36 n n C1D O4D AR6 sing 37 n n C2' O2' AR6 sing 38 n n C2' C3' AR6 sing 39 n n C2D O2D AR6 sing 40 n n C2D C3D AR6 sing 41 n n C3' O3' AR6 sing 42 n n C3' C4' AR6 sing 43 n n C3D O3D AR6 sing 44 n n C3D C4D AR6 sing 45 n n C4' O4' AR6 sing 46 n n C4' C5' AR6 sing 47 n n C4D O4D AR6 sing 48 n n C4D C5D AR6 sing 49 n n C5' O5' AR6 sing 50 n n C5D O5D AR6 sing 51 n n C2 H2 AR6 sing 52 n n N6 HN6 AR6 sing 53 n n N6 HN6A AR6 sing 54 n n C8 H8 AR6 sing 55 n n C1' H1' AR6 sing 56 n n C1D H1D AR6 sing 57 n n C2' H2' AR6 sing 58 n n O2' HO2' AR6 sing 59 n n C2D H2D AR6 sing 60 n n O2D HO2D AR6 sing 61 n n C3' H3' AR6 sing 62 n n O3' HO3' AR6 sing 63 n n C3D H3D AR6 sing 64 n n O3D HO3D AR6 sing 65 n n C4' H4' AR6 sing 66 n n C4D H4D AR6 sing 67 n n C5' H5' AR6 sing 68 n n C5' "H5'A" AR6 sing 69 n n C5D H5D AR6 sing 70 n n C5D H5DA AR6 sing 71 n n O1A H1A AR6 sing 72 n n O1B H1B AR6 sing 73 n n O1D HD1 AR6 sing 74 n n # _atom_sites.entry_id 3X0K _atom_sites.fract_transf_matrix[1][1] 0.020143 _atom_sites.fract_transf_matrix[1][2] 0.01163 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023259 _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] 0.008427 _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 AR6 A 1 201 1 AR6 APR . C 3 GOL A 1 202 1 GOL GOL . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 52 HOH HOH . D 4 HOH A 52 352 53 HOH HOH . D 4 HOH A 53 353 54 HOH HOH . D 4 HOH A 54 354 55 HOH HOH . D 4 HOH A 55 355 56 HOH HOH . D 4 HOH A 56 356 57 HOH HOH . D 4 HOH A 57 357 58 HOH HOH . D 4 HOH A 58 358 59 HOH HOH . D 4 HOH A 59 359 60 HOH HOH . D 4 HOH A 60 360 61 HOH HOH . D 4 HOH A 61 361 64 HOH HOH . D 4 HOH A 62 362 65 HOH HOH . D 4 HOH A 63 363 67 HOH HOH . D 4 HOH A 64 364 68 HOH HOH . D 4 HOH A 65 365 70 HOH HOH . D 4 HOH A 66 366 72 HOH HOH . D 4 HOH A 67 367 73 HOH HOH . D 4 HOH A 68 368 75 HOH HOH . D 4 HOH A 69 369 76 HOH HOH . D 4 HOH A 70 370 80 HOH HOH . D 4 HOH A 71 371 81 HOH HOH . D 4 HOH A 72 372 82 HOH HOH . D 4 HOH A 73 373 83 HOH HOH . D 4 HOH A 74 374 84 HOH HOH . D 4 HOH A 75 375 85 HOH HOH . D 4 HOH A 76 376 86 HOH HOH . D 4 HOH A 77 377 88 HOH HOH . D 4 HOH A 78 378 89 HOH HOH . D 4 HOH A 79 379 90 HOH HOH . D 4 HOH A 80 380 93 HOH HOH . D 4 HOH A 81 381 96 HOH HOH . D 4 HOH A 82 382 97 HOH HOH . D 4 HOH A 83 383 98 HOH HOH . D 4 HOH A 84 384 99 HOH HOH . D 4 HOH A 85 385 101 HOH HOH . D 4 HOH A 86 386 102 HOH HOH . D 4 HOH A 87 387 104 HOH HOH . D 4 HOH A 88 388 105 HOH HOH . D 4 HOH A 89 389 106 HOH HOH . D 4 HOH A 90 390 107 HOH HOH . D 4 HOH A 91 391 108 HOH HOH . D 4 HOH A 92 392 111 HOH HOH . D 4 HOH A 93 393 112 HOH HOH . D 4 HOH A 94 394 114 HOH HOH . D 4 HOH A 95 395 115 HOH HOH . D 4 HOH A 96 396 116 HOH HOH . D 4 HOH A 97 397 117 HOH HOH . D 4 HOH A 98 398 118 HOH HOH . D 4 HOH A 99 399 120 HOH HOH . D 4 HOH A 100 400 122 HOH HOH . D 4 HOH A 101 401 123 HOH HOH . D 4 HOH A 102 402 127 HOH HOH . D 4 HOH A 103 403 130 HOH HOH . D 4 HOH A 104 404 131 HOH HOH . D 4 HOH A 105 405 132 HOH HOH . D 4 HOH A 106 406 133 HOH HOH . D 4 HOH A 107 407 135 HOH HOH . D 4 HOH A 108 408 136 HOH HOH . D 4 HOH A 109 409 137 HOH HOH . D 4 HOH A 110 410 138 HOH HOH . D 4 HOH A 111 411 139 HOH HOH . D 4 HOH A 112 412 140 HOH HOH . D 4 HOH A 113 413 141 HOH HOH . D 4 HOH A 114 414 143 HOH HOH . D 4 HOH A 115 415 148 HOH HOH . D 4 HOH A 116 416 149 HOH HOH . D 4 HOH A 117 417 155 HOH HOH . D 4 HOH A 118 418 157 HOH HOH . D 4 HOH A 119 419 158 HOH HOH . D 4 HOH A 120 420 159 HOH HOH . D 4 HOH A 121 421 160 HOH HOH . D 4 HOH A 122 422 166 HOH HOH . D 4 HOH A 123 423 167 HOH HOH . D 4 HOH A 124 424 168 HOH HOH . D 4 HOH A 125 425 169 HOH HOH . D 4 HOH A 126 426 170 HOH HOH . D 4 HOH A 127 427 171 HOH HOH . D 4 HOH A 128 428 172 HOH HOH . D 4 HOH A 129 429 173 HOH HOH . D 4 HOH A 130 430 174 HOH HOH . D 4 HOH A 131 431 175 HOH HOH . D 4 HOH A 132 432 176 HOH HOH . D 4 HOH A 133 433 177 HOH HOH . D 4 HOH A 134 434 178 HOH HOH . D 4 HOH A 135 435 179 HOH HOH . D 4 HOH A 136 436 180 HOH HOH . D 4 HOH A 137 437 181 HOH HOH . D 4 HOH A 138 438 182 HOH HOH . D 4 HOH A 139 439 183 HOH HOH . D 4 HOH A 140 440 184 HOH HOH . D 4 HOH A 141 441 185 HOH HOH . D 4 HOH A 142 442 186 HOH HOH . D 4 HOH A 143 443 187 HOH HOH . D 4 HOH A 144 444 188 HOH HOH . D 4 HOH A 145 445 189 HOH HOH . D 4 HOH A 146 446 190 HOH HOH . D 4 HOH A 147 447 191 HOH HOH . D 4 HOH A 148 448 192 HOH HOH . D 4 HOH A 149 449 193 HOH HOH . D 4 HOH A 150 450 194 HOH HOH . D 4 HOH A 151 451 195 HOH HOH . D 4 HOH A 152 452 196 HOH HOH . D 4 HOH A 153 453 197 HOH HOH . D 4 HOH A 154 454 198 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 N N1 AR6 . A . B 2 -1.778 -6.174 -10.203 0.75 12.17 ? N1 AR6 201 A 1 HETATM 2 C C2 AR6 . A . B 2 -2.107 -5.462 -11.292 0.75 13.04 ? C2 AR6 201 A 1 HETATM 3 N N3 AR6 . A . B 2 -3.069 -5.803 -12.194 0.75 13.22 ? N3 AR6 201 A 1 HETATM 4 C C4 AR6 . A . B 2 -3.408 -7.114 -12.129 0.75 12.69 ? C4 AR6 201 A 1 HETATM 5 C C5 AR6 . A . B 2 -2.942 -8.003 -11.117 0.75 11.98 ? C5 AR6 201 A 1 HETATM 6 C C6 AR6 . A . B 2 -2.197 -7.444 -10.022 0.75 11 ? C6 AR6 201 A 1 HETATM 7 N N6 AR6 . A . B 2 -1.698 -8.226 -9.011 0.75 11.82 ? N6 AR6 201 A 1 HETATM 8 N N7 AR6 . A . B 2 -3.407 -9.288 -11.355 0.75 14.13 ? N7 AR6 201 A 1 HETATM 9 C C8 AR6 . A . B 2 -4.167 -9.118 -12.452 0.75 15.4 ? C8 AR6 201 A 1 HETATM 10 N N9 AR6 . A . B 2 -4.119 -7.87 -12.974 0.75 15.75 ? N9 AR6 201 A 1 HETATM 11 P PA AR6 . A . B 2 -9.078 -10.869 -14.217 0.75 10.04 ? PA AR6 201 A 1 HETATM 12 P PB AR6 . A . B 2 -7.921 -12.632 -12.168 0.75 7.68 ? PB AR6 201 A 1 HETATM 13 C C1' AR6 . A . B 2 -4.967 -7.327 -14.062 0.75 15.23 ? C1' AR6 201 A 1 HETATM 14 O O1A AR6 . A . B 2 -8.305 -11.53 -15.179 0.75 14.08 ? O1A AR6 201 A 1 HETATM 15 O O1B AR6 . A . B 2 -8.044 -13.94 -12.869 0.75 10.46 ? O1B AR6 201 A 1 HETATM 16 C C1D AR6 . A . B 2 -7.693 -14.905 -8.012 0.75 6.17 ? C1D AR6 201 A 1 HETATM 17 O O1D AR6 . A . B 2 -8.024 -15.505 -6.768 0.75 7.15 ? O1D AR6 201 A 1 HETATM 18 C C2' AR6 . A . B 2 -4.842 -8.174 -15.3 0.75 17.95 ? C2' AR6 201 A 1 HETATM 19 O O2' AR6 . A . B 2 -4.467 -7.373 -16.399 0.75 25.32 ? O2' AR6 201 A 1 HETATM 20 O O2A AR6 . A . B 2 -10.521 -10.574 -14.409 0.75 10.22 ? O2A AR6 201 A 1 HETATM 21 O O2B AR6 . A . B 2 -6.57 -11.996 -12.104 0.75 8.96 ? O2B AR6 201 A 1 HETATM 22 C C2D AR6 . A . B 2 -7.557 -13.429 -7.936 0.75 6.61 ? C2D AR6 201 A 1 HETATM 23 O O2D AR6 . A . B 2 -6.853 -12.912 -6.839 0.75 7.52 ? O2D AR6 201 A 1 HETATM 24 C C3' AR6 . A . B 2 -6.269 -8.622 -15.615 0.75 17.87 ? C3' AR6 201 A 1 HETATM 25 O O3' AR6 . A . B 2 -6.506 -8.743 -16.996 0.75 26.21 ? O3' AR6 201 A 1 HETATM 26 O O3A AR6 . A . B 2 -8.977 -11.61 -12.818 0.75 8.01 ? O3A AR6 201 A 1 HETATM 27 C C3D AR6 . A . B 2 -9.021 -12.973 -7.98 0.75 5.95 ? C3D AR6 201 A 1 HETATM 28 O O3D AR6 . A . B 2 -9.607 -13.196 -6.691 0.75 6.58 ? O3D AR6 201 A 1 HETATM 29 C C4' AR6 . A . B 2 -7.131 -7.669 -14.88 0.75 16.94 ? C4' AR6 201 A 1 HETATM 30 O O4' AR6 . A . B 2 -6.36 -7.304 -13.746 0.75 15.88 ? O4' AR6 201 A 1 HETATM 31 C C4D AR6 . A . B 2 -9.623 -13.909 -8.991 0.75 6.61 ? C4D AR6 201 A 1 HETATM 32 O O4D AR6 . A . B 2 -8.771 -15.094 -8.953 0.75 6.35 ? O4D AR6 201 A 1 HETATM 33 C C5' AR6 . A . B 2 -8.522 -8.216 -14.576 0.75 16.86 ? C5' AR6 201 A 1 HETATM 34 O O5' AR6 . A . B 2 -8.421 -9.389 -13.868 0.75 13.39 ? O5' AR6 201 A 1 HETATM 35 C C5D AR6 . A . B 2 -9.702 -13.404 -10.386 0.75 6.73 ? C5D AR6 201 A 1 HETATM 36 O O5D AR6 . A . B 2 -8.471 -12.694 -10.708 0.75 7.84 ? O5D AR6 201 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #