data_6RGA # _model_server_result.job_id BNmlvczdeFVnCT5S_GDkHQ _model_server_result.datetime_utc '2024-11-28 15:29:20' _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 6rga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6RGA # _exptl.entry_id 6RGA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 569.53 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{R},3~{S},4~{R},5~{R})-2-(aminomethyl)-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]oxolane-3,4-diol _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 90 _cell.entry_id 6RGA _cell.length_a 63.18 _cell.length_b 74.73 _cell.length_c 118.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 1 2 A,B,C,D 1 3 A,B,C,D 1 4 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 63.18 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.18 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C23 H27 N11 O7' _chem_comp.formula_weight 569.53 _chem_comp.id K3E _chem_comp.mon_nstd_flag . _chem_comp.name (2~{R},3~{S},4~{R},5~{R})-2-(aminomethyl)-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]oxolane-3,4-diol _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 K3E sing 193 n n N7 C5 K3E sing 194 n y N7 C8 K3E doub 195 n y C6 C5 K3E doub 196 n y C6 N1 K3E sing 197 n y C5 C4 K3E sing 198 n y C8 N9 K3E sing 199 n y N1 C2 K3E doub 200 n y C2' O2' K3E sing 201 n n C2' C3' K3E sing 202 n n C2' C1' K3E sing 203 n n C4 N9 K3E sing 204 n y C4 N3 K3E doub 205 n y N9 C1' K3E sing 206 n n C3' O3' K3E sing 207 n n C3' C4' K3E sing 208 n n C2 N3 K3E sing 209 n y C1' O4' K3E sing 210 n n O4' C4' K3E sing 211 n n C4' C5' K3E sing 212 n n C5' O5' K3E sing 213 n n NBB CAY K3E sing 214 n n CAY NAX K3E doub 215 n y CAY CAZ K3E sing 216 n y O5' CAP K3E sing 217 n n NBA CAZ K3E sing 218 n y NBA CAS K3E doub 219 n y NAX CAW K3E sing 220 n y CAZ CAU K3E doub 221 n y CAS CAR K3E sing 222 n n CAS NAT K3E sing 223 n y CAR CAQ K3E trip 224 n n CAQ CAP K3E sing 225 n n CAW NAV K3E doub 226 n y CAU NAT K3E sing 227 n y CAU NAV K3E sing 228 n y OBK CBJ K3E sing 229 n n NAT CBC K3E sing 230 n n CBJ CBC K3E sing 231 n n CBJ CBH K3E sing 232 n n CBC OBD K3E sing 233 n n CBH OBI K3E sing 234 n n CBH CBE K3E sing 235 n n OBD CBE K3E sing 236 n n CBE CBF K3E sing 237 n n CBF NBG K3E sing 238 n n C2 H1 K3E sing 239 n n C1' H2 K3E sing 240 n n C2' H3 K3E sing 241 n n C3' H4 K3E sing 242 n n C4' H5 K3E sing 243 n n C5' H6 K3E sing 244 n n C5' H7 K3E sing 245 n n C8 H8 K3E sing 246 n n CAP H9 K3E sing 247 n n CAP H10 K3E sing 248 n n CAW H11 K3E sing 249 n n CBC H12 K3E sing 250 n n CBE H13 K3E sing 251 n n CBF H14 K3E sing 252 n n CBF H15 K3E sing 253 n n CBH H16 K3E sing 254 n n CBJ H17 K3E sing 255 n n N6 H18 K3E sing 256 n n N6 H19 K3E sing 257 n n NBB H20 K3E sing 258 n n NBB H21 K3E sing 259 n n NBG H22 K3E sing 260 n n NBG H23 K3E sing 261 n n O2' H25 K3E sing 262 n n O3' H26 K3E sing 263 n n OBI H27 K3E sing 264 n n OBK H28 K3E sing 265 n n # _atom_sites.entry_id 6RGA _atom_sites.fract_transf_matrix[1][1] 0.015828 _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] 0.013382 _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] 0.008422 _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 CIT A 1 301 1 CIT CIT . C 3 K3E A 1 302 1 K3E PDB . D 4 HOH A 1 401 118 HOH HOH . D 4 HOH A 2 402 88 HOH HOH . D 4 HOH A 3 403 119 HOH HOH . D 4 HOH A 4 404 25 HOH HOH . D 4 HOH A 5 405 82 HOH HOH . D 4 HOH A 6 406 19 HOH HOH . D 4 HOH A 7 407 15 HOH HOH . D 4 HOH A 8 408 17 HOH HOH . D 4 HOH A 9 409 71 HOH HOH . D 4 HOH A 10 410 18 HOH HOH . D 4 HOH A 11 411 7 HOH HOH . D 4 HOH A 12 412 34 HOH HOH . D 4 HOH A 13 413 3 HOH HOH . D 4 HOH A 14 414 2 HOH HOH . D 4 HOH A 15 415 77 HOH HOH . D 4 HOH A 16 416 35 HOH HOH . D 4 HOH A 17 417 12 HOH HOH . D 4 HOH A 18 418 1 HOH HOH . D 4 HOH A 19 419 29 HOH HOH . D 4 HOH A 20 420 16 HOH HOH . D 4 HOH A 21 421 79 HOH HOH . D 4 HOH A 22 422 42 HOH HOH . D 4 HOH A 23 423 99 HOH HOH . D 4 HOH A 24 424 9 HOH HOH . D 4 HOH A 25 425 5 HOH HOH . D 4 HOH A 26 426 23 HOH HOH . D 4 HOH A 27 427 80 HOH HOH . D 4 HOH A 28 428 26 HOH HOH . D 4 HOH A 29 429 14 HOH HOH . D 4 HOH A 30 430 81 HOH HOH . D 4 HOH A 31 431 4 HOH HOH . D 4 HOH A 32 432 43 HOH HOH . D 4 HOH A 33 433 13 HOH HOH . D 4 HOH A 34 434 98 HOH HOH . D 4 HOH A 35 435 21 HOH HOH . D 4 HOH A 36 436 44 HOH HOH . D 4 HOH A 37 437 53 HOH HOH . D 4 HOH A 38 438 68 HOH HOH . D 4 HOH A 39 439 41 HOH HOH . D 4 HOH A 40 440 45 HOH HOH . D 4 HOH A 41 441 96 HOH HOH . D 4 HOH A 42 442 20 HOH HOH . D 4 HOH A 43 443 28 HOH HOH . D 4 HOH A 44 444 51 HOH HOH . D 4 HOH A 45 445 87 HOH HOH . D 4 HOH A 46 446 22 HOH HOH . D 4 HOH A 47 447 40 HOH HOH . D 4 HOH A 48 448 102 HOH HOH . D 4 HOH A 49 449 11 HOH HOH . D 4 HOH A 50 450 100 HOH HOH . D 4 HOH A 51 451 89 HOH HOH . D 4 HOH A 52 452 70 HOH HOH . D 4 HOH A 53 453 107 HOH HOH . D 4 HOH A 54 454 6 HOH HOH . D 4 HOH A 55 455 46 HOH HOH . D 4 HOH A 56 456 32 HOH HOH . D 4 HOH A 57 457 27 HOH HOH . D 4 HOH A 58 458 52 HOH HOH . D 4 HOH A 59 459 10 HOH HOH . D 4 HOH A 60 460 8 HOH HOH . D 4 HOH A 61 461 113 HOH HOH . D 4 HOH A 62 462 117 HOH HOH . D 4 HOH A 63 463 38 HOH HOH . D 4 HOH A 64 464 101 HOH HOH . D 4 HOH A 65 465 108 HOH HOH . D 4 HOH A 66 466 56 HOH HOH . D 4 HOH A 67 467 72 HOH HOH . D 4 HOH A 68 468 67 HOH HOH . D 4 HOH A 69 469 39 HOH HOH . D 4 HOH A 70 470 116 HOH HOH . D 4 HOH A 71 471 61 HOH HOH . D 4 HOH A 72 472 65 HOH HOH . D 4 HOH A 73 473 55 HOH HOH . D 4 HOH A 74 474 114 HOH HOH . D 4 HOH A 75 475 103 HOH HOH . D 4 HOH A 76 476 58 HOH HOH . D 4 HOH A 77 477 50 HOH HOH . D 4 HOH A 78 478 97 HOH HOH . D 4 HOH A 79 479 86 HOH HOH . D 4 HOH A 80 480 85 HOH HOH . D 4 HOH A 81 481 75 HOH HOH . D 4 HOH A 82 482 110 HOH HOH . D 4 HOH A 83 483 120 HOH HOH . D 4 HOH A 84 484 59 HOH HOH . D 4 HOH A 85 485 112 HOH HOH . D 4 HOH A 86 486 76 HOH HOH . D 4 HOH A 87 487 94 HOH HOH . D 4 HOH A 88 488 60 HOH HOH . D 4 HOH A 89 489 84 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 K3E . . . C 3 19.918 5.356 8.432 1 29.02 ? C2 K3E 302 A 1 HETATM 2 C C4 K3E . . . C 3 17.926 6.28 8.192 1 31.35 ? C4 K3E 302 A 1 HETATM 3 C C5 K3E . . . C 3 17.533 5.204 7.502 1 31.48 ? C5 K3E 302 A 1 HETATM 4 C C6 K3E . . . C 3 18.41 4.181 7.279 1 30.8 ? C6 K3E 302 A 1 HETATM 5 N N9 K3E . . . C 3 16.942 7.09 8.266 1 33.21 ? N9 K3E 302 A 1 HETATM 6 C C1' K3E . . . C 3 16.881 8.354 8.885 1 30.25 ? C1' K3E 302 A 1 HETATM 7 C C2' K3E . . . C 3 16.711 9.479 7.863 1 28.47 ? C2' K3E 302 A 1 HETATM 8 C C3' K3E . . . C 3 15.481 10.211 8.404 1 28.62 ? C3' K3E 302 A 1 HETATM 9 C C4' K3E . . . C 3 15.403 9.687 9.82 1 30.85 ? C4' K3E 302 A 1 HETATM 10 C C5' K3E . . . C 3 14.003 9.935 10.496 1 32.59 ? C5' K3E 302 A 1 HETATM 11 C C8 K3E . . . C 3 15.958 6.526 7.637 1 32.26 ? C8 K3E 302 A 1 HETATM 12 C CAP K3E . . . C 3 14.287 11.123 12.793 1 34.66 ? CAP K3E 302 A 1 HETATM 13 C CAQ K3E . . . C 3 15.714 11.375 12.749 1 34.07 ? CAQ K3E 302 A 1 HETATM 14 C CAR K3E . . . C 3 16.843 11.568 12.707 1 32.72 ? CAR K3E 302 A 1 HETATM 15 C CAS K3E . . . C 3 18.23 11.703 12.707 1 31.55 ? CAS K3E 302 A 1 HETATM 16 C CAU K3E . . . C 3 20.217 11.35 13.109 1 30.81 ? CAU K3E 302 A 1 HETATM 17 C CAW K3E . . . C 3 22.429 11.609 13.007 1 27.8 ? CAW K3E 302 A 1 HETATM 18 C CAY K3E . . . C 3 21.229 13.101 11.903 1 30.45 ? CAY K3E 302 A 1 HETATM 19 C CAZ K3E . . . C 3 20.101 12.44 12.323 1 32.39 ? CAZ K3E 302 A 1 HETATM 20 C CBC K3E . . . C 3 18.597 9.818 14.091 1 33.05 ? CBC K3E 302 A 1 HETATM 21 C CBE K3E . . . C 3 19.329 9.246 16.139 1 32.37 ? CBE K3E 302 A 1 HETATM 22 C CBF K3E . . . C 3 20.82 9.37 16.281 1 30.95 ? CBF K3E 302 A 1 HETATM 23 C CBH K3E . . . C 3 19.246 8.017 15.311 1 34.91 ? CBH K3E 302 A 1 HETATM 24 C CBJ K3E . . . C 3 19.296 8.57 13.922 1 33.12 ? CBJ K3E 302 A 1 HETATM 25 N N1 K3E . . . C 3 19.59 4.309 7.78 1 30.15 ? N1 K3E 302 A 1 HETATM 26 N N3 K3E . . . C 3 19.128 6.32 8.628 1 29.89 ? N3 K3E 302 A 1 HETATM 27 N N6 K3E . . . C 3 18.113 3.111 6.626 1 28.8 ? N6 K3E 302 A 1 HETATM 28 N N7 K3E . . . C 3 16.321 5.399 7.173 1 32.21 ? N7 K3E 302 A 1 HETATM 29 N NAT K3E . . . C 3 19.037 10.923 13.314 1 29.93 ? NAT K3E 302 A 1 HETATM 30 N NAV K3E . . . C 3 21.415 10.952 13.43 1 28.35 ? NAV K3E 302 A 1 HETATM 31 N NAX K3E . . . C 3 22.371 12.637 12.254 1 28.98 ? NAX K3E 302 A 1 HETATM 32 N NBA K3E . . . C 3 18.861 12.623 12.117 1 31.42 ? NBA K3E 302 A 1 HETATM 33 N NBB K3E . . . C 3 21.182 14.148 11.174 1 29.93 ? NBB K3E 302 A 1 HETATM 34 N NBG K3E . . . C 3 21.096 10.593 16.984 1 30.43 ? NBG K3E 302 A 1 HETATM 35 O O2' K3E . . . C 3 17.798 10.287 7.873 1 27.51 ? O2' K3E 302 A 1 HETATM 36 O O3' K3E . . . C 3 15.67 11.557 8.424 1 27.42 ? O3' K3E 302 A 1 HETATM 37 O O4' K3E . . . C 3 15.734 8.369 9.622 1 30.77 ? O4' K3E 302 A 1 HETATM 38 O O5' K3E . . . C 3 13.923 9.982 11.955 1 36.25 ? O5' K3E 302 A 1 HETATM 39 O OBD K3E . . . C 3 18.846 10.253 15.389 1 33.02 ? OBD K3E 302 A 1 HETATM 40 O OBI K3E . . . C 3 18.031 7.437 15.576 1 40.05 ? OBI K3E 302 A 1 HETATM 41 O OBK K3E . . . C 3 18.501 7.863 13.122 1 32.64 ? OBK K3E 302 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 41 #