data_3AC9 # _model_server_result.job_id qZajvkpc4RGJvWDliAUGpQ _model_server_result.datetime_utc '2024-10-19 01:34:13' _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 3ac9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 3AC9 # _exptl.entry_id 3AC9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)" _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 121.59 _cell.angle_gamma 90 _cell.entry_id 3AC9 _cell.length_a 113.24 _cell.length_b 40.442 _cell.length_c 99.418 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AC9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 D N N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id 8GD _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate" # 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 8GD sing 1 n n N1 C6 8GD sing 2 n n C2 N2 8GD sing 3 n n C2 N3 8GD doub 4 n n N3 C4 8GD sing 5 n n C4 C5 8GD doub 6 n n C4 N9 8GD sing 7 n n C5 C6 8GD sing 8 n n C5 N7 8GD sing 9 n n C6 O6 8GD doub 10 n n N7 C8 8GD sing 11 n n C8 O8 8GD doub 12 n n C8 N9 8GD sing 13 n n N9 C1' 8GD sing 14 n n PA O1A 8GD doub 15 n n PA O2A 8GD sing 16 n n PA O3A 8GD sing 17 n n PA O5' 8GD sing 18 n n PB O1B 8GD sing 19 n n PB O2B 8GD doub 20 n n PB O3A 8GD sing 21 n n PB O3B 8GD sing 22 n n C1' C2' 8GD sing 23 n n C1' O4' 8GD sing 24 n n C2' C3' 8GD sing 25 n n C3' O3' 8GD sing 26 n n C3' C4' 8GD sing 27 n n C4' O4' 8GD sing 28 n n C4' C5' 8GD sing 29 n n C5' O5' 8GD sing 30 n n N1 HN1 8GD sing 31 n n N2 HN2 8GD sing 32 n n N2 HN2A 8GD sing 33 n n N7 HN7 8GD sing 34 n n C1' H1' 8GD sing 35 n n O1B HO1B 8GD sing 36 n n C2' H2' 8GD sing 37 n n C2' "H2'A" 8GD sing 38 n n O2A HO2A 8GD sing 39 n n C3' H3' 8GD sing 40 n n O3' HO3' 8GD sing 41 n n O3B HO3B 8GD sing 42 n n C4' H4' 8GD sing 43 n n C5' H5' 8GD sing 44 n n C5' "H5'A" 8GD sing 45 n n # _atom_sites.entry_id 3AC9 _atom_sites.fract_transf_matrix[1][1] 0.008831 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005431 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024727 _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] 0.011808 _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 8GD A 1 2 2 8GD 8GD . D 2 8GD B 1 1 1 8GD 8GD . E 3 MN B 1 209 209 MN MN . F 3 MN B 1 2 2 MN MN . G 4 HOH A 1 300 300 HOH HOH . G 4 HOH A 2 301 301 HOH HOH . G 4 HOH A 3 302 302 HOH HOH . G 4 HOH A 4 303 303 HOH HOH . G 4 HOH A 5 304 304 HOH HOH . G 4 HOH A 6 305 305 HOH HOH . G 4 HOH A 7 306 306 HOH HOH . G 4 HOH A 8 307 307 HOH HOH . G 4 HOH A 9 308 308 HOH HOH . G 4 HOH A 10 309 309 HOH HOH . G 4 HOH A 11 310 310 HOH HOH . G 4 HOH A 12 311 311 HOH HOH . G 4 HOH A 13 312 312 HOH HOH . G 4 HOH A 14 313 313 HOH HOH . G 4 HOH A 15 314 314 HOH HOH . G 4 HOH A 16 315 315 HOH HOH . G 4 HOH A 17 316 316 HOH HOH . G 4 HOH A 18 317 317 HOH HOH . G 4 HOH A 19 318 318 HOH HOH . G 4 HOH A 20 319 319 HOH HOH . G 4 HOH A 21 320 320 HOH HOH . G 4 HOH A 22 321 321 HOH HOH . G 4 HOH A 23 322 322 HOH HOH . G 4 HOH A 24 323 323 HOH HOH . G 4 HOH A 25 324 324 HOH HOH . G 4 HOH A 26 325 325 HOH HOH . G 4 HOH A 27 326 326 HOH HOH . G 4 HOH A 28 327 327 HOH HOH . G 4 HOH A 29 328 328 HOH HOH . G 4 HOH A 30 329 329 HOH HOH . G 4 HOH A 31 330 330 HOH HOH . G 4 HOH A 32 331 331 HOH HOH . G 4 HOH A 33 332 332 HOH HOH . G 4 HOH A 34 333 333 HOH HOH . G 4 HOH A 35 334 334 HOH HOH . G 4 HOH A 36 335 335 HOH HOH . G 4 HOH A 37 336 336 HOH HOH . G 4 HOH A 38 337 337 HOH HOH . G 4 HOH A 39 338 338 HOH HOH . G 4 HOH A 40 339 339 HOH HOH . G 4 HOH A 41 340 340 HOH HOH . G 4 HOH A 42 341 341 HOH HOH . G 4 HOH A 43 342 342 HOH HOH . G 4 HOH A 44 343 343 HOH HOH . G 4 HOH A 45 344 344 HOH HOH . G 4 HOH A 46 345 345 HOH HOH . G 4 HOH A 47 346 346 HOH HOH . G 4 HOH A 48 347 347 HOH HOH . G 4 HOH A 49 348 348 HOH HOH . G 4 HOH A 50 349 349 HOH HOH . G 4 HOH A 51 350 350 HOH HOH . G 4 HOH A 52 351 351 HOH HOH . G 4 HOH A 53 352 352 HOH HOH . G 4 HOH A 54 353 353 HOH HOH . G 4 HOH A 55 354 354 HOH HOH . G 4 HOH A 56 355 355 HOH HOH . G 4 HOH A 57 356 356 HOH HOH . G 4 HOH A 58 357 357 HOH HOH . G 4 HOH A 59 358 358 HOH HOH . G 4 HOH A 60 359 359 HOH HOH . G 4 HOH A 61 360 360 HOH HOH . G 4 HOH A 62 361 361 HOH HOH . G 4 HOH A 63 362 362 HOH HOH . G 4 HOH A 64 363 363 HOH HOH . G 4 HOH A 65 364 364 HOH HOH . G 4 HOH A 66 365 365 HOH HOH . G 4 HOH A 67 366 366 HOH HOH . G 4 HOH A 68 367 367 HOH HOH . G 4 HOH A 69 368 368 HOH HOH . G 4 HOH A 70 369 369 HOH HOH . G 4 HOH A 71 370 370 HOH HOH . G 4 HOH A 72 371 371 HOH HOH . G 4 HOH A 73 372 372 HOH HOH . G 4 HOH A 74 373 373 HOH HOH . G 4 HOH A 75 374 374 HOH HOH . G 4 HOH A 76 375 375 HOH HOH . G 4 HOH A 77 376 376 HOH HOH . G 4 HOH A 78 377 377 HOH HOH . G 4 HOH A 79 378 378 HOH HOH . G 4 HOH A 80 379 379 HOH HOH . H 4 HOH B 1 380 380 HOH HOH . H 4 HOH B 2 381 381 HOH HOH . H 4 HOH B 3 382 382 HOH HOH . H 4 HOH B 4 383 383 HOH HOH . H 4 HOH B 5 384 384 HOH HOH . H 4 HOH B 6 385 385 HOH HOH . H 4 HOH B 7 386 386 HOH HOH . H 4 HOH B 8 387 387 HOH HOH . H 4 HOH B 9 388 388 HOH HOH . H 4 HOH B 10 389 389 HOH HOH . H 4 HOH B 11 390 390 HOH HOH . H 4 HOH B 12 391 391 HOH HOH . H 4 HOH B 13 392 392 HOH HOH . H 4 HOH B 14 393 393 HOH HOH . H 4 HOH B 15 394 394 HOH HOH . H 4 HOH B 16 395 395 HOH HOH . H 4 HOH B 17 396 396 HOH HOH . H 4 HOH B 18 397 397 HOH HOH . H 4 HOH B 19 398 398 HOH HOH . H 4 HOH B 20 399 399 HOH HOH . H 4 HOH B 21 400 400 HOH HOH . H 4 HOH B 22 401 401 HOH HOH . H 4 HOH B 23 402 402 HOH HOH . H 4 HOH B 24 403 403 HOH HOH . H 4 HOH B 25 404 404 HOH HOH . H 4 HOH B 26 405 405 HOH HOH . H 4 HOH B 27 406 406 HOH HOH . H 4 HOH B 28 407 407 HOH HOH . H 4 HOH B 29 408 408 HOH HOH . H 4 HOH B 30 409 409 HOH HOH . H 4 HOH B 31 410 410 HOH HOH . H 4 HOH B 32 411 411 HOH HOH . H 4 HOH B 33 412 412 HOH HOH . H 4 HOH B 34 413 413 HOH HOH . H 4 HOH B 35 414 414 HOH HOH . H 4 HOH B 36 415 415 HOH HOH . H 4 HOH B 37 416 416 HOH HOH . H 4 HOH B 38 417 417 HOH HOH . H 4 HOH B 39 418 418 HOH HOH . H 4 HOH B 40 419 419 HOH HOH . H 4 HOH B 41 420 420 HOH HOH . H 4 HOH B 42 421 421 HOH HOH . H 4 HOH B 43 422 422 HOH HOH . H 4 HOH B 44 423 423 HOH HOH . H 4 HOH B 45 424 424 HOH HOH . H 4 HOH B 46 425 425 HOH HOH . H 4 HOH B 47 426 426 HOH HOH . H 4 HOH B 48 427 427 HOH HOH . H 4 HOH B 49 428 428 HOH HOH . H 4 HOH B 50 429 429 HOH HOH . H 4 HOH B 51 430 430 HOH HOH . H 4 HOH B 52 431 431 HOH HOH . H 4 HOH B 53 432 432 HOH HOH . H 4 HOH B 54 433 433 HOH HOH . H 4 HOH B 55 434 434 HOH HOH . H 4 HOH B 56 435 435 HOH HOH . H 4 HOH B 57 436 436 HOH HOH . H 4 HOH B 58 437 437 HOH HOH . H 4 HOH B 59 438 438 HOH HOH . H 4 HOH B 60 439 439 HOH HOH . H 4 HOH B 61 440 440 HOH HOH . H 4 HOH B 62 441 441 HOH HOH . H 4 HOH B 63 442 442 HOH HOH . H 4 HOH B 64 443 443 HOH HOH . H 4 HOH B 65 444 444 HOH HOH . H 4 HOH B 66 445 445 HOH HOH . H 4 HOH B 67 446 446 HOH HOH . H 4 HOH B 68 447 447 HOH HOH . H 4 HOH B 69 448 448 HOH HOH . H 4 HOH B 70 449 449 HOH HOH . H 4 HOH B 71 450 450 HOH HOH . H 4 HOH B 72 451 451 HOH HOH . H 4 HOH B 73 452 452 HOH HOH . H 4 HOH B 74 453 453 HOH HOH . H 4 HOH B 75 454 454 HOH HOH . H 4 HOH B 76 455 455 HOH HOH . H 4 HOH B 77 456 456 HOH HOH . H 4 HOH B 78 457 457 HOH HOH . H 4 HOH B 79 458 458 HOH HOH . H 4 HOH B 80 459 459 HOH HOH . H 4 HOH B 81 460 460 HOH HOH . H 4 HOH B 82 461 461 HOH HOH . H 4 HOH B 83 462 462 HOH HOH . H 4 HOH B 84 463 463 HOH HOH . H 4 HOH B 85 464 464 HOH HOH . H 4 HOH B 86 465 465 HOH HOH . H 4 HOH B 87 466 466 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 8GD . . . D 2 -18.192 22.624 78.146 1 48.99 ? N1 8GD 1 B 1 HETATM 2 C C2 8GD . . . D 2 -18.256 21.427 77.469 1 50.29 ? C2 8GD 1 B 1 HETATM 3 N N2 8GD . . . D 2 -17.109 20.959 76.949 1 46.79 ? N2 8GD 1 B 1 HETATM 4 N N3 8GD . . . D 2 -19.374 20.733 77.315 1 51.45 ? N3 8GD 1 B 1 HETATM 5 C C4 8GD . . . D 2 -20.436 21.347 77.898 1 53.06 ? C4 8GD 1 B 1 HETATM 6 C C5 8GD . . . D 2 -20.472 22.536 78.585 1 49.18 ? C5 8GD 1 B 1 HETATM 7 C C6 8GD . . . D 2 -19.276 23.265 78.745 1 44.09 ? C6 8GD 1 B 1 HETATM 8 O O6 8GD . . . D 2 -19.116 24.342 79.328 1 46.69 ? O6 8GD 1 B 1 HETATM 9 N N7 8GD . . . D 2 -21.758 22.811 79.018 1 52.83 ? N7 8GD 1 B 1 HETATM 10 C C8 8GD . . . D 2 -22.482 21.805 78.598 1 54.42 ? C8 8GD 1 B 1 HETATM 11 O O8 8GD . . . D 2 -23.692 21.742 78.822 1 53.88 ? O8 8GD 1 B 1 HETATM 12 N N9 8GD . . . D 2 -21.728 20.879 77.907 1 52.57 ? N9 8GD 1 B 1 HETATM 13 P PA 8GD . . . D 2 -23.546 19.018 71.774 1 71.1 ? PA 8GD 1 B 1 HETATM 14 P PB 8GD . . . D 2 -25.834 17.918 73.282 1 60.12 ? PB 8GD 1 B 1 HETATM 15 C C1' 8GD . . . D 2 -22.131 19.617 77.26 1 58.44 ? C1' 8GD 1 B 1 HETATM 16 O O1A 8GD . . . D 2 -23.452 18.326 70.463 1 47.02 ? O1A 8GD 1 B 1 HETATM 17 O O1B 8GD . . . D 2 -26.638 18.043 72.058 1 51.02 ? O1B 8GD 1 B 1 HETATM 18 C C2' 8GD . . . D 2 -23.557 19.621 76.739 1 59.39 ? C2' 8GD 1 B 1 HETATM 19 O O2A 8GD . . . D 2 -24.145 20.39 71.822 1 60.45 ? O2A 8GD 1 B 1 HETATM 20 O O2B 8GD . . . D 2 -26.09 18.797 74.4 1 69.53 ? O2B 8GD 1 B 1 HETATM 21 C C3' 8GD . . . D 2 -23.459 18.647 75.571 1 65.07 ? C3' 8GD 1 B 1 HETATM 22 O O3' 8GD . . . D 2 -23.516 17.312 76.064 1 69.95 ? O3' 8GD 1 B 1 HETATM 23 O O3A 8GD . . . D 2 -24.319 18.009 72.807 1 64.73 ? O3A 8GD 1 B 1 HETATM 24 O O3B 8GD . . . D 2 -25.973 16.426 73.804 1 53.21 ? O3B 8GD 1 B 1 HETATM 25 C C4' 8GD . . . D 2 -22.058 18.895 75.008 1 64.2 ? C4' 8GD 1 B 1 HETATM 26 O O4' 8GD . . . D 2 -21.293 19.439 76.117 1 68.51 ? O4' 8GD 1 B 1 HETATM 27 C C5' 8GD . . . D 2 -21.99 19.788 73.77 1 58.56 ? C5' 8GD 1 B 1 HETATM 28 O O5' 8GD . . . D 2 -22.167 18.981 72.578 1 63.42 ? O5' 8GD 1 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #