data_5KM6 # _model_server_result.job_id 961TyXoViVev_kCDfnE4Hg _model_server_result.datetime_utc '2024-11-14 07:11:42' _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 5km6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5KM6 # _exptl.entry_id 5KM6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 489.422 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic 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 90 _cell.entry_id 5KM6 _cell.length_a 40.163 _cell.length_b 40.163 _cell.length_c 144.239 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KM6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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' 7_555 y,x,-z 0 1 0 1 0 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 'C20 H24 N7 O6 P' _chem_comp.formula_weight 489.422 _chem_comp.id 6US _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms TpAra-Ad # 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 C15 C14 6US doub 1 n y C15 C16 6US sing 2 n y C14 C13 6US sing 3 n y C16 C12 6US doub 4 n y O2P P 6US doub 5 n n C13 C11 6US doub 6 n y C12 C11 6US sing 7 n y C12 C7 6US sing 8 n y C1 C3 6US sing 9 n n C1 N1P 6US sing 10 n n C11 N10 6US sing 11 n y C3 C7 6US sing 12 n n P N1P 6US sing 13 n n P O5' 6US sing 14 n n P O3P 6US sing 15 n n C7 C9 6US doub 16 n y O5' C5' 6US sing 17 n n N10 C9 6US sing 18 n y O3' C3' 6US sing 19 n n C5' C4' 6US sing 20 n n C4' C3' 6US sing 21 n n C4' O4' 6US sing 22 n n C3' C2' 6US sing 23 n n O4' C1' 6US sing 24 n n C2' C1' 6US sing 25 n n C2' O2' 6US sing 26 n n C1' N9 6US sing 27 n n N3 C4 6US doub 28 n y N3 C2 6US sing 29 n y N9 C4 6US sing 30 n y N9 C8 6US sing 31 n y C4 C5 6US sing 32 n y C2 N1 6US doub 33 n y C8 N7 6US doub 34 n y C5 N7 6US sing 35 n y C5 C6 6US doub 36 n y N1 C6 6US sing 37 n y C6 N6 6US sing 38 n n C1 H1 6US sing 39 n n C1 H2 6US sing 40 n n C8 H3 6US sing 41 n n C16 H4 6US sing 42 n n C2 H5 6US sing 43 n n C3 H6 6US sing 44 n n C3 H7 6US sing 45 n n C14 H8 6US sing 46 n n O3P H9 6US sing 47 n n N1P H10 6US sing 48 n n C5' H11 6US sing 49 n n C5' H12 6US sing 50 n n C4' H13 6US sing 51 n n C3' H14 6US sing 52 n n O3' H15 6US sing 53 n n C2' H16 6US sing 54 n n O2' H17 6US sing 55 n n C1' H18 6US sing 56 n n N6 H19 6US sing 57 n n N6 H20 6US sing 58 n n C9 H21 6US sing 59 n n N10 H22 6US sing 60 n n C13 H23 6US sing 61 n n C15 H24 6US sing 62 n n # _atom_sites.entry_id 5KM6 _atom_sites.fract_transf_matrix[1][1] 0.024899 _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] 0.024899 _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] 0.006933 _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 6US A 1 201 1 6US 064 . C 3 HOH A 1 301 82 HOH HOH . C 3 HOH A 2 302 62 HOH HOH . C 3 HOH A 3 303 2 HOH HOH . C 3 HOH A 4 304 49 HOH HOH . C 3 HOH A 5 305 32 HOH HOH . C 3 HOH A 6 306 53 HOH HOH . C 3 HOH A 7 307 28 HOH HOH . C 3 HOH A 8 308 58 HOH HOH . C 3 HOH A 9 309 8 HOH HOH . C 3 HOH A 10 310 59 HOH HOH . C 3 HOH A 11 311 11 HOH HOH . C 3 HOH A 12 312 36 HOH HOH . C 3 HOH A 13 313 15 HOH HOH . C 3 HOH A 14 314 26 HOH HOH . C 3 HOH A 15 315 71 HOH HOH . C 3 HOH A 16 316 87 HOH HOH . C 3 HOH A 17 317 24 HOH HOH . C 3 HOH A 18 318 83 HOH HOH . C 3 HOH A 19 319 17 HOH HOH . C 3 HOH A 20 320 64 HOH HOH . C 3 HOH A 21 321 50 HOH HOH . C 3 HOH A 22 322 66 HOH HOH . C 3 HOH A 23 323 14 HOH HOH . C 3 HOH A 24 324 13 HOH HOH . C 3 HOH A 25 325 23 HOH HOH . C 3 HOH A 26 326 30 HOH HOH . C 3 HOH A 27 327 38 HOH HOH . C 3 HOH A 28 328 45 HOH HOH . C 3 HOH A 29 329 27 HOH HOH . C 3 HOH A 30 330 25 HOH HOH . C 3 HOH A 31 331 39 HOH HOH . C 3 HOH A 32 332 10 HOH HOH . C 3 HOH A 33 333 5 HOH HOH . C 3 HOH A 34 334 7 HOH HOH . C 3 HOH A 35 335 52 HOH HOH . C 3 HOH A 36 336 9 HOH HOH . C 3 HOH A 37 337 3 HOH HOH . C 3 HOH A 38 338 12 HOH HOH . C 3 HOH A 39 339 46 HOH HOH . C 3 HOH A 40 340 19 HOH HOH . C 3 HOH A 41 341 44 HOH HOH . C 3 HOH A 42 342 4 HOH HOH . C 3 HOH A 43 343 35 HOH HOH . C 3 HOH A 44 344 89 HOH HOH . C 3 HOH A 45 345 40 HOH HOH . C 3 HOH A 46 346 84 HOH HOH . C 3 HOH A 47 347 76 HOH HOH . C 3 HOH A 48 348 18 HOH HOH . C 3 HOH A 49 349 81 HOH HOH . C 3 HOH A 50 350 16 HOH HOH . C 3 HOH A 51 351 85 HOH HOH . C 3 HOH A 52 352 6 HOH HOH . C 3 HOH A 53 353 21 HOH HOH . C 3 HOH A 54 354 54 HOH HOH . C 3 HOH A 55 355 73 HOH HOH . C 3 HOH A 56 356 61 HOH HOH . C 3 HOH A 57 357 88 HOH HOH . C 3 HOH A 58 358 79 HOH HOH . C 3 HOH A 59 359 70 HOH HOH . C 3 HOH A 60 360 22 HOH HOH . C 3 HOH A 61 361 37 HOH HOH . C 3 HOH A 62 362 80 HOH HOH . C 3 HOH A 63 363 20 HOH HOH . C 3 HOH A 64 364 43 HOH HOH . C 3 HOH A 65 365 91 HOH HOH . C 3 HOH A 66 366 1 HOH HOH . C 3 HOH A 67 367 34 HOH HOH . C 3 HOH A 68 368 31 HOH HOH . C 3 HOH A 69 369 33 HOH HOH . C 3 HOH A 70 370 42 HOH HOH . C 3 HOH A 71 371 41 HOH HOH . C 3 HOH A 72 372 60 HOH HOH . C 3 HOH A 73 373 90 HOH HOH . C 3 HOH A 74 374 48 HOH HOH . C 3 HOH A 75 375 63 HOH HOH . C 3 HOH A 76 376 29 HOH HOH . C 3 HOH A 77 377 47 HOH HOH . C 3 HOH A 78 378 75 HOH HOH . C 3 HOH A 79 379 65 HOH HOH . C 3 HOH A 80 380 92 HOH HOH . C 3 HOH A 81 381 67 HOH HOH . C 3 HOH A 82 382 57 HOH HOH . C 3 HOH A 83 383 69 HOH HOH . C 3 HOH A 84 384 86 HOH HOH . C 3 HOH A 85 385 55 HOH HOH . C 3 HOH A 86 386 56 HOH HOH . C 3 HOH A 87 387 51 HOH HOH . C 3 HOH A 88 388 72 HOH HOH . C 3 HOH A 89 389 77 HOH HOH . C 3 HOH A 90 390 78 HOH HOH . C 3 HOH A 91 391 74 HOH HOH . C 3 HOH A 92 392 68 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 C1 6US . . . B 2 14.662 10.786 9.651 1 10.67 ? C1 6US 201 A 1 HETATM 2 C C5 6US . . . B 2 9.181 11.872 17.934 1 11.78 ? C5 6US 201 A 1 HETATM 3 C C6 6US . . . B 2 7.987 12.164 18.735 1 14.04 ? C6 6US 201 A 1 HETATM 4 C C7 6US . . . B 2 16.904 11.726 10.424 1 9.7 ? C7 6US 201 A 1 HETATM 5 C C8 6US . . . B 2 11.053 11.344 16.98 1 12.47 ? C8 6US 201 A 1 HETATM 6 C C16 6US . . . B 2 17.827 11.689 7.939 1 12.08 ? C16 6US 201 A 1 HETATM 7 C C2 6US . . . B 2 6.966 13.097 16.801 1 13.68 ? C2 6US 201 A 1 HETATM 8 C C3 6US . . . B 2 15.396 11.908 10.375 1 11.51 ? C3 6US 201 A 1 HETATM 9 C C12 6US . . . B 2 17.904 11.646 9.325 1 10.78 ? C12 6US 201 A 1 HETATM 10 C C14 6US . . . B 2 20.237 11.446 7.817 1 12.51 ? C14 6US 201 A 1 HETATM 11 O O3P 6US . . . B 2 13.483 7.388 11.261 1 9.49 ? O3P 6US 201 A 1 HETATM 12 P P 6US . . . B 2 13.249 8.6 10.42 1 10.55 ? P 6US 201 A 1 HETATM 13 N N1P 6US . . . B 2 14.693 9.559 10.422 1 11.09 ? N1P 6US 201 A 1 HETATM 14 O O2P 6US . . . B 2 12.802 8.428 8.993 1 10.36 ? O2P 6US 201 A 1 HETATM 15 O O5' 6US . . . B 2 12.154 9.567 11.094 1 10.53 ? O5' 6US 201 A 1 HETATM 16 C C5' 6US . . . B 2 11.995 9.616 12.504 1 11.93 ? C5' 6US 201 A 1 HETATM 17 C C4' 6US . . . B 2 11.256 10.914 12.785 1 9.92 ? C4' 6US 201 A 1 HETATM 18 C C3' 6US . . . B 2 12.16 12.143 12.817 1 10.3 ? C3' 6US 201 A 1 HETATM 19 O O3' 6US . . . B 2 11.743 13.033 11.777 1 11.6 ? O3' 6US 201 A 1 HETATM 20 C C2' 6US . . . B 2 11.927 12.783 14.185 1 12.09 ? C2' 6US 201 A 1 HETATM 21 O O2' 6US . . . B 2 13.001 12.442 15.068 1 13.78 ? O2' 6US 201 A 1 HETATM 22 C C1' 6US . . . B 2 10.627 12.118 14.595 1 11.43 ? C1' 6US 201 A 1 HETATM 23 O O4' 6US . . . B 2 10.713 10.789 14.087 1 11.31 ? O4' 6US 201 A 1 HETATM 24 N N9 6US . . . B 2 10.318 11.941 16.022 1 10.9 ? N9 6US 201 A 1 HETATM 25 C C4 6US . . . B 2 9.128 12.27 16.528 1 11.6 ? C4 6US 201 A 1 HETATM 26 N N7 6US . . . B 2 10.382 11.307 18.159 1 12.94 ? N7 6US 201 A 1 HETATM 27 N N3 6US . . . B 2 8.03 12.877 16.013 1 12.01 ? N3 6US 201 A 1 HETATM 28 N N1 6US . . . B 2 6.953 12.749 18.097 1 12.93 ? N1 6US 201 A 1 HETATM 29 N N6 6US . . . B 2 7.926 11.834 20.046 1 14.45 ? N6 6US 201 A 1 HETATM 30 C C9 6US . . . B 2 17.638 11.614 11.593 1 11.42 ? C9 6US 201 A 1 HETATM 31 N N10 6US . . . B 2 18.97 11.476 11.322 1 11.73 ? N10 6US 201 A 1 HETATM 32 C C11 6US . . . B 2 19.204 11.496 9.998 1 10.66 ? C11 6US 201 A 1 HETATM 33 C C13 6US . . . B 2 20.347 11.396 9.21 1 13.34 ? C13 6US 201 A 1 HETATM 34 C C15 6US . . . B 2 18.999 11.595 7.187 1 12.43 ? C15 6US 201 A 1 # _model_server_stats.io_time_ms 62 _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 6 _model_server_stats.element_count 34 #