data_3AC9
#
_model_server_result.job_id            4VRelZL0LhzwVd371Ag9PA 
_model_server_result.datetime_utc      '2024-11-23 11:37:43' 
_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          3ac9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":2}' 
#
_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 . . . C 2 0.708 16.688 73.52 1 55.63 ? N1 8GD 2 A 1 
HETATM 2 C C2 8GD . . . C 2 0.028 17.161 72.413 1 60.74 ? C2 8GD 2 A 1 
HETATM 3 N N2 8GD . . . C 2 -1.252 17.539 72.616 1 55.52 ? N2 8GD 2 A 1 
HETATM 4 N N3 8GD . . . C 2 0.567 17.256 71.195 1 59.54 ? N3 8GD 2 A 1 
HETATM 5 C C4 8GD . . . C 2 1.859 16.829 71.175 1 59.63 ? C4 8GD 2 A 1 
HETATM 6 C C5 8GD . . . C 2 2.61 16.342 72.222 1 59.28 ? C5 8GD 2 A 1 
HETATM 7 C C6 8GD . . . C 2 2.029 16.245 73.509 1 54.89 ? C6 8GD 2 A 1 
HETATM 8 O O6 8GD . . . C 2 2.557 15.835 74.551 1 56.78 ? O6 8GD 2 A 1 
HETATM 9 N N7 8GD . . . C 2 3.892 16.012 71.798 1 62.14 ? N7 8GD 2 A 1 
HETATM 10 C C8 8GD . . . C 2 3.908 16.294 70.521 1 62.13 ? C8 8GD 2 A 1 
HETATM 11 O O8 8GD . . . C 2 4.915 16.112 69.837 1 59.38 ? O8 8GD 2 A 1 
HETATM 12 N N9 8GD . . . C 2 2.699 16.801 70.077 1 63.1 ? N9 8GD 2 A 1 
HETATM 13 C C1' 8GD . . . C 2 2.312 17.232 68.712 1 63.44 ? C1' 8GD 2 A 1 
HETATM 14 C C2' 8GD . . . C 2 3.36 18 67.916 1 60.36 ? C2' 8GD 2 A 1 
HETATM 15 C C3' 8GD . . . C 2 4.069 16.914 67.111 1 64.37 ? C3' 8GD 2 A 1 
HETATM 16 O O3' 8GD . . . C 2 4.49 17.423 65.846 1 60.9 ? O3' 8GD 2 A 1 
HETATM 17 C C4' 8GD . . . C 2 2.96 15.899 66.867 1 60.13 ? C4' 8GD 2 A 1 
HETATM 18 O O4' 8GD . . . C 2 2.019 16.062 67.955 1 61.04 ? O4' 8GD 2 A 1 
HETATM 19 C C5' 8GD . . . C 2 3.437 14.46 66.813 1 61.03 ? C5' 8GD 2 A 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           216 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           19 
#