data_6R0T # _model_server_result.job_id JehrO3VeOSbhSAGkbQ118A _model_server_result.datetime_utc '2024-10-20 01:26:40' _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 6r0t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":201}' # _entry.id 6R0T # _exptl.entry_id 6R0T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 561.332 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate' _entity.pdbx_number_of_molecules 2 _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 6R0T _cell.length_a 46.673 _cell.length_b 71.441 _cell.length_c 98.97 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6R0T _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,K 1 1 B,I,J,L 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 I N N # _chem_comp.formula 'C15 H25 N5 O14 P2' _chem_comp.formula_weight 561.332 _chem_comp.id JNT _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen 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 N1 C2 JNT doub 188 n y N1 C6 JNT sing 189 n y N6 C6 JNT sing 190 n n C2 N3 JNT sing 191 n y C6 C5 JNT doub 192 n y N3 C4 JNT doub 193 n y C5 C4 JNT sing 194 n y C5 N7 JNT sing 195 n y C4 N9 JNT sing 196 n y N7 C8 JNT doub 197 n y O2' C2' JNT sing 198 n n N9 C8 JNT sing 199 n y N9 C1' JNT sing 200 n n C1' C2' JNT sing 201 n n C1' O4' JNT sing 202 n n C2' C3' JNT sing 203 n n O4' C4' JNT sing 204 n n C3' O3' JNT sing 205 n n C3' C4' JNT sing 206 n n C4' C5' JNT sing 207 n n O5' C5' JNT sing 208 n n O5' PA JNT sing 209 n n O1A PA JNT doub 210 n n O2A PA JNT sing 211 n n PA O3A JNT sing 212 n n O2C C2A JNT sing 213 n n O3A PB JNT sing 214 n n O4C C4A JNT sing 215 n n C2A C1A JNT sing 216 n n C2A C3A JNT sing 217 n n C1A O1C JNT sing 218 n n O1B PB JNT doub 219 n n PB O5A JNT sing 220 n n PB O2B JNT sing 221 n n C4A C3A JNT sing 222 n n C4A C5A JNT sing 223 n n O5A C5A JNT sing 224 n n C5' H1 JNT sing 225 n n C5' H2 JNT sing 226 n n C4' H3 JNT sing 227 n n C3' H4 JNT sing 228 n n O3' H5 JNT sing 229 n n C2' H6 JNT sing 230 n n O2' H7 JNT sing 231 n n C1' H8 JNT sing 232 n n C8 H9 JNT sing 233 n n C2 H10 JNT sing 234 n n N6 H11 JNT sing 235 n n N6 H12 JNT sing 236 n n O1C H13 JNT sing 237 n n C1A H14 JNT sing 238 n n C1A H15 JNT sing 239 n n C2A H16 JNT sing 240 n n O2C H17 JNT sing 241 n n C3A H18 JNT sing 242 n n O3C H19 JNT sing 243 n n C4A H20 JNT sing 244 n n O4C H21 JNT sing 245 n n C5A H22 JNT sing 246 n n C5A H23 JNT sing 247 n n O2B H24 JNT sing 248 n n O2A H25 JNT sing 249 n n C3A O3C JNT sing 250 n n # _atom_sites.entry_id 6R0T _atom_sites.fract_transf_matrix[1][1] 0.021426 _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] 0.013998 _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] 0.010104 _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 C 2 JNT A 1 201 2 JNT ZZ9 . D 3 EDO A 1 202 4 EDO EDO . E 3 EDO A 1 203 5 EDO EDO . F 3 EDO A 1 204 6 EDO EDO . G 4 ACT A 1 205 7 ACT ACT . H 4 ACT A 1 206 8 ACT ACT . I 2 JNT B 1 201 1 JNT ZZ9 . J 3 EDO B 1 202 3 EDO EDO . K 5 HOH A 1 301 138 HOH HOH . K 5 HOH A 2 302 129 HOH HOH . K 5 HOH A 3 303 152 HOH HOH . K 5 HOH A 4 304 11 HOH HOH . K 5 HOH A 5 305 144 HOH HOH . K 5 HOH A 6 306 88 HOH HOH . K 5 HOH A 7 307 76 HOH HOH . K 5 HOH A 8 308 128 HOH HOH . K 5 HOH A 9 309 95 HOH HOH . K 5 HOH A 10 310 101 HOH HOH . K 5 HOH A 11 311 61 HOH HOH . K 5 HOH A 12 312 35 HOH HOH . K 5 HOH A 13 313 186 HOH HOH . K 5 HOH A 14 314 69 HOH HOH . K 5 HOH A 15 315 108 HOH HOH . K 5 HOH A 16 316 8 HOH HOH . K 5 HOH A 17 317 77 HOH HOH . K 5 HOH A 18 318 71 HOH HOH . K 5 HOH A 19 319 7 HOH HOH . K 5 HOH A 20 320 33 HOH HOH . K 5 HOH A 21 321 114 HOH HOH . K 5 HOH A 22 322 6 HOH HOH . K 5 HOH A 23 323 55 HOH HOH . K 5 HOH A 24 324 159 HOH HOH . K 5 HOH A 25 325 3 HOH HOH . K 5 HOH A 26 326 51 HOH HOH . K 5 HOH A 27 327 46 HOH HOH . K 5 HOH A 28 328 2 HOH HOH . K 5 HOH A 29 329 174 HOH HOH . K 5 HOH A 30 330 16 HOH HOH . K 5 HOH A 31 331 133 HOH HOH . K 5 HOH A 32 332 29 HOH HOH . K 5 HOH A 33 333 32 HOH HOH . K 5 HOH A 34 334 30 HOH HOH . K 5 HOH A 35 335 70 HOH HOH . K 5 HOH A 36 336 93 HOH HOH . K 5 HOH A 37 337 154 HOH HOH . K 5 HOH A 38 338 132 HOH HOH . K 5 HOH A 39 339 102 HOH HOH . K 5 HOH A 40 340 66 HOH HOH . K 5 HOH A 41 341 74 HOH HOH . K 5 HOH A 42 342 167 HOH HOH . K 5 HOH A 43 343 65 HOH HOH . K 5 HOH A 44 344 91 HOH HOH . K 5 HOH A 45 345 98 HOH HOH . K 5 HOH A 46 346 58 HOH HOH . K 5 HOH A 47 347 148 HOH HOH . K 5 HOH A 48 348 60 HOH HOH . K 5 HOH A 49 349 26 HOH HOH . K 5 HOH A 50 350 181 HOH HOH . K 5 HOH A 51 351 22 HOH HOH . K 5 HOH A 52 352 9 HOH HOH . K 5 HOH A 53 353 182 HOH HOH . K 5 HOH A 54 354 59 HOH HOH . K 5 HOH A 55 355 99 HOH HOH . K 5 HOH A 56 356 106 HOH HOH . K 5 HOH A 57 357 126 HOH HOH . K 5 HOH A 58 358 146 HOH HOH . K 5 HOH A 59 359 149 HOH HOH . K 5 HOH A 60 360 45 HOH HOH . K 5 HOH A 61 361 19 HOH HOH . K 5 HOH A 62 362 44 HOH HOH . K 5 HOH A 63 363 147 HOH HOH . K 5 HOH A 64 364 1 HOH HOH . K 5 HOH A 65 365 131 HOH HOH . K 5 HOH A 66 366 153 HOH HOH . K 5 HOH A 67 367 75 HOH HOH . K 5 HOH A 68 368 43 HOH HOH . K 5 HOH A 69 369 169 HOH HOH . K 5 HOH A 70 370 36 HOH HOH . K 5 HOH A 71 371 104 HOH HOH . K 5 HOH A 72 372 150 HOH HOH . K 5 HOH A 73 373 53 HOH HOH . K 5 HOH A 74 374 103 HOH HOH . K 5 HOH A 75 375 15 HOH HOH . K 5 HOH A 76 376 12 HOH HOH . K 5 HOH A 77 377 63 HOH HOH . K 5 HOH A 78 378 5 HOH HOH . K 5 HOH A 79 379 4 HOH HOH . K 5 HOH A 80 380 176 HOH HOH . K 5 HOH A 81 381 52 HOH HOH . K 5 HOH A 82 382 120 HOH HOH . K 5 HOH A 83 383 127 HOH HOH . K 5 HOH A 84 384 187 HOH HOH . K 5 HOH A 85 385 143 HOH HOH . K 5 HOH A 86 386 161 HOH HOH . K 5 HOH A 87 387 125 HOH HOH . K 5 HOH A 88 388 151 HOH HOH . K 5 HOH A 89 389 189 HOH HOH . K 5 HOH A 90 390 121 HOH HOH . K 5 HOH A 91 391 180 HOH HOH . K 5 HOH A 92 392 190 HOH HOH . K 5 HOH A 93 393 179 HOH HOH . K 5 HOH A 94 394 142 HOH HOH . K 5 HOH A 95 395 113 HOH HOH . K 5 HOH A 96 396 172 HOH HOH . K 5 HOH A 97 397 112 HOH HOH . K 5 HOH A 98 398 130 HOH HOH . K 5 HOH A 99 399 134 HOH HOH . K 5 HOH A 100 400 124 HOH HOH . K 5 HOH A 101 401 175 HOH HOH . L 5 HOH B 1 301 123 HOH HOH . L 5 HOH B 2 302 166 HOH HOH . L 5 HOH B 3 303 137 HOH HOH . L 5 HOH B 4 304 84 HOH HOH . L 5 HOH B 5 305 145 HOH HOH . L 5 HOH B 6 306 48 HOH HOH . L 5 HOH B 7 307 50 HOH HOH . L 5 HOH B 8 308 81 HOH HOH . L 5 HOH B 9 309 155 HOH HOH . L 5 HOH B 10 310 18 HOH HOH . L 5 HOH B 11 311 62 HOH HOH . L 5 HOH B 12 312 85 HOH HOH . L 5 HOH B 13 313 94 HOH HOH . L 5 HOH B 14 314 78 HOH HOH . L 5 HOH B 15 315 31 HOH HOH . L 5 HOH B 16 316 21 HOH HOH . L 5 HOH B 17 317 92 HOH HOH . L 5 HOH B 18 318 160 HOH HOH . L 5 HOH B 19 319 105 HOH HOH . L 5 HOH B 20 320 13 HOH HOH . L 5 HOH B 21 321 49 HOH HOH . L 5 HOH B 22 322 136 HOH HOH . L 5 HOH B 23 323 162 HOH HOH . L 5 HOH B 24 324 10 HOH HOH . L 5 HOH B 25 325 165 HOH HOH . L 5 HOH B 26 326 157 HOH HOH . L 5 HOH B 27 327 168 HOH HOH . L 5 HOH B 28 328 17 HOH HOH . L 5 HOH B 29 329 100 HOH HOH . L 5 HOH B 30 330 87 HOH HOH . L 5 HOH B 31 331 34 HOH HOH . L 5 HOH B 32 332 79 HOH HOH . L 5 HOH B 33 333 83 HOH HOH . L 5 HOH B 34 334 163 HOH HOH . L 5 HOH B 35 335 86 HOH HOH . L 5 HOH B 36 336 23 HOH HOH . L 5 HOH B 37 337 80 HOH HOH . L 5 HOH B 38 338 14 HOH HOH . L 5 HOH B 39 339 28 HOH HOH . L 5 HOH B 40 340 42 HOH HOH . L 5 HOH B 41 341 38 HOH HOH . L 5 HOH B 42 342 173 HOH HOH . L 5 HOH B 43 343 39 HOH HOH . L 5 HOH B 44 344 96 HOH HOH . L 5 HOH B 45 345 170 HOH HOH . L 5 HOH B 46 346 97 HOH HOH . L 5 HOH B 47 347 64 HOH HOH . L 5 HOH B 48 348 82 HOH HOH . L 5 HOH B 49 349 135 HOH HOH . L 5 HOH B 50 350 171 HOH HOH . L 5 HOH B 51 351 25 HOH HOH . L 5 HOH B 52 352 107 HOH HOH . L 5 HOH B 53 353 41 HOH HOH . L 5 HOH B 54 354 37 HOH HOH . L 5 HOH B 55 355 20 HOH HOH . L 5 HOH B 56 356 188 HOH HOH . L 5 HOH B 57 357 24 HOH HOH . L 5 HOH B 58 358 47 HOH HOH . L 5 HOH B 59 359 109 HOH HOH . L 5 HOH B 60 360 57 HOH HOH . L 5 HOH B 61 361 56 HOH HOH . L 5 HOH B 62 362 27 HOH HOH . L 5 HOH B 63 363 110 HOH HOH . L 5 HOH B 64 364 54 HOH HOH . L 5 HOH B 65 365 72 HOH HOH . L 5 HOH B 66 366 40 HOH HOH . L 5 HOH B 67 367 122 HOH HOH . L 5 HOH B 68 368 158 HOH HOH . L 5 HOH B 69 369 185 HOH HOH . L 5 HOH B 70 370 89 HOH HOH . L 5 HOH B 71 371 68 HOH HOH . L 5 HOH B 72 372 73 HOH HOH . L 5 HOH B 73 373 119 HOH HOH . L 5 HOH B 74 374 183 HOH HOH . L 5 HOH B 75 375 156 HOH HOH . L 5 HOH B 76 376 116 HOH HOH . L 5 HOH B 77 377 178 HOH HOH . L 5 HOH B 78 378 177 HOH HOH . L 5 HOH B 79 379 117 HOH HOH . L 5 HOH B 80 380 90 HOH HOH . L 5 HOH B 81 381 111 HOH HOH . L 5 HOH B 82 382 184 HOH HOH . L 5 HOH B 83 383 164 HOH HOH . L 5 HOH B 84 384 67 HOH HOH . L 5 HOH B 85 385 139 HOH HOH . L 5 HOH B 86 386 140 HOH HOH . L 5 HOH B 87 387 141 HOH HOH . L 5 HOH B 88 388 118 HOH HOH . L 5 HOH B 89 389 115 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' JNT . . . I 2 -6.637 52.444 14.783 1 46.63 ? O5' JNT 201 B 1 HETATM 2 C C5' JNT . . . I 2 -5.838 51.333 14.439 1 50.24 ? C5' JNT 201 B 1 HETATM 3 C C4' JNT . . . I 2 -5.656 50.541 15.712 1 54.38 ? C4' JNT 201 B 1 HETATM 4 O O4' JNT . . . I 2 -4.784 51.223 16.615 1 51.35 ? O4' JNT 201 B 1 HETATM 5 C C3' JNT . . . I 2 -6.98 50.351 16.433 1 54.52 ? C3' JNT 201 B 1 HETATM 6 O O3' JNT . . . I 2 -6.94 49.001 16.902 1 59.12 ? O3' JNT 201 B 1 HETATM 7 C C2' JNT . . . I 2 -6.949 51.386 17.553 1 54.01 ? C2' JNT 201 B 1 HETATM 8 O O2' JNT . . . I 2 -7.651 50.99 18.726 1 58.99 ? O2' JNT 201 B 1 HETATM 9 C C1' JNT . . . I 2 -5.467 51.457 17.855 1 52.99 ? C1' JNT 201 B 1 HETATM 10 N N9 JNT . . . I 2 -4.948 52.746 18.387 1 50.7 ? N9 JNT 201 B 1 HETATM 11 C C8 JNT . . . I 2 -5.478 53.973 18.259 1 49.08 ? C8 JNT 201 B 1 HETATM 12 N N7 JNT . . . I 2 -4.689 54.899 18.852 1 48.46 ? N7 JNT 201 B 1 HETATM 13 C C5 JNT . . . I 2 -3.624 54.261 19.364 1 49.34 ? C5 JNT 201 B 1 HETATM 14 C C4 JNT . . . I 2 -3.802 52.841 19.053 1 47.83 ? C4 JNT 201 B 1 HETATM 15 N N3 JNT . . . I 2 -2.862 51.96 19.463 1 51.08 ? N3 JNT 201 B 1 HETATM 16 C C2 JNT . . . I 2 -1.782 52.382 20.15 1 50.71 ? C2 JNT 201 B 1 HETATM 17 N N1 JNT . . . I 2 -1.568 53.676 20.473 1 47.02 ? N1 JNT 201 B 1 HETATM 18 C C6 JNT . . . I 2 -2.428 54.647 20.131 1 44.66 ? C6 JNT 201 B 1 HETATM 19 N N6 JNT . . . I 2 -2.209 55.939 20.445 1 45.79 ? N6 JNT 201 B 1 HETATM 20 O O1C JNT . . . I 2 -5.02 56.905 12.531 1 57.61 ? O1C JNT 201 B 1 HETATM 21 C C1A JNT . . . I 2 -5.827 57.753 12.154 1 63.3 ? C1A JNT 201 B 1 HETATM 22 C C2A JNT . . . I 2 -5.86 58.273 10.723 1 60.92 ? C2A JNT 201 B 1 HETATM 23 O O2C JNT . . . I 2 -6.133 59.677 10.761 1 73.76 ? O2C JNT 201 B 1 HETATM 24 C C3A JNT . . . I 2 -6.92 57.717 9.784 1 55 ? C3A JNT 201 B 1 HETATM 25 O O3C JNT . . . I 2 -7.731 58.861 9.413 1 54.53 ? O3C JNT 201 B 1 HETATM 26 C C4A JNT . . . I 2 -7.787 56.559 10.295 1 48.67 ? C4A JNT 201 B 1 HETATM 27 O O4C JNT . . . I 2 -8.171 56.741 11.666 1 53.48 ? O4C JNT 201 B 1 HETATM 28 C C5A JNT . . . I 2 -7.086 55.203 10.163 1 46.5 ? C5A JNT 201 B 1 HETATM 29 O O5A JNT . . . I 2 -7.977 54.168 10.607 1 41.66 ? O5A JNT 201 B 1 HETATM 30 P PB JNT . . . I 2 -7.435 52.733 10.995 1 40.77 ? PB JNT 201 B 1 HETATM 31 O O2B JNT . . . I 2 -6.441 52.209 9.975 1 40.63 ? O2B JNT 201 B 1 HETATM 32 O O1B JNT . . . I 2 -8.63 51.858 11.357 1 39.62 ? O1B JNT 201 B 1 HETATM 33 O O3A JNT . . . I 2 -6.573 52.939 12.315 1 43.14 ? O3A JNT 201 B 1 HETATM 34 P PA JNT . . . I 2 -6.956 53.609 13.752 1 44.79 ? PA JNT 201 B 1 HETATM 35 O O1A JNT . . . I 2 -8.418 53.8 13.857 1 46.89 ? O1A JNT 201 B 1 HETATM 36 O O2A JNT . . . I 2 -5.99 54.732 14.024 1 47.96 ? O2A JNT 201 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #