data_8J99
#
_model_server_result.job_id            MsIKQN-vHhPJLCFN1mhOPw 
_model_server_result.datetime_utc      '2025-06-16 10:43:26' 
_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          8j99 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":801}' 
#
_entry.id    8J99 
#
_exptl.entry_id    8J99 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              849.635 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 
_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    ? 
_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
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
#
_chem_comp.formula           'C26 H42 N7 O17 P3 S' 
_chem_comp.formula_weight    849.635 
_chem_comp.id                TW3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate' 
_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
O6 P1 TW3 doub 332 n n 
O7 P1 TW3 sing 333 n n 
P1 O8 TW3 sing 334 n n 
P1 O5 TW3 sing 335 n n 
O8 P2 TW3 sing 336 n n 
O9 P2 TW3 doub 337 n n 
O17 P3 TW3 doub 338 n n 
O11 P2 TW3 sing 339 n n 
O11 C17 TW3 sing 340 n n 
P2 O10 TW3 sing 341 n n 
O5 C16 TW3 sing 342 n n 
C17 C18 TW3 sing 343 n n 
C16 C13 TW3 sing 344 n n 
O14 P3 TW3 sing 345 n n 
O14 C26 TW3 sing 346 n n 
P3 O15 TW3 sing 347 n n 
P3 O16 TW3 sing 348 n n 
C18 C26 TW3 sing 349 n n 
C18 O12 TW3 sing 350 n n 
C26 C25 TW3 sing 351 n n 
C13 C14 TW3 sing 352 n n 
C13 C15 TW3 sing 353 n n 
C13 C12 TW3 sing 354 n n 
O4 C12 TW3 sing 355 n n 
O12 C19 TW3 sing 356 n n 
C12 C11 TW3 sing 357 n n 
C25 O13 TW3 sing 358 n n 
C25 C19 TW3 sing 359 n n 
C19 N3 TW3 sing 360 n n 
C11 O3 TW3 doub 361 n n 
C11 N2 TW3 sing 362 n n 
N7 C24 TW3 doub 363 n y 
N7 C23 TW3 sing 364 n y 
N3 C24 TW3 sing 365 n y 
N3 C20 TW3 sing 366 n y 
N2 C10 TW3 sing 367 n n 
C24 C21 TW3 sing 368 n y 
C23 N6 TW3 doub 369 n y 
C20 N4 TW3 doub 370 n y 
C21 N4 TW3 sing 371 n y 
C21 C22 TW3 doub 372 n y 
N6 C22 TW3 sing 373 n y 
C10 C9 TW3 sing 374 n n 
C22 N5 TW3 sing 375 n n 
C9 C8 TW3 sing 376 n n 
C8 N1 TW3 sing 377 n n 
C8 O2 TW3 doub 378 n n 
N1 C7 TW3 sing 379 n n 
C7 C6 TW3 sing 380 n n 
S1 C6 TW3 sing 381 n n 
S1 C5 TW3 sing 382 n n 
C4 C5 TW3 sing 383 n n 
C4 C2 TW3 doub 384 n n 
C5 O1 TW3 doub 385 n n 
C1 C2 TW3 sing 386 n n 
C2 C3 TW3 sing 387 n n 
C1 H1 TW3 sing 388 n n 
C1 H2 TW3 sing 389 n n 
C1 H3 TW3 sing 390 n n 
C10 H4 TW3 sing 391 n n 
C10 H5 TW3 sing 392 n n 
C12 H6 TW3 sing 393 n n 
C14 H7 TW3 sing 394 n n 
C14 H8 TW3 sing 395 n n 
C14 H9 TW3 sing 396 n n 
C15 H10 TW3 sing 397 n n 
C15 H11 TW3 sing 398 n n 
C15 H12 TW3 sing 399 n n 
C16 H13 TW3 sing 400 n n 
C16 H14 TW3 sing 401 n n 
C17 H15 TW3 sing 402 n n 
C17 H16 TW3 sing 403 n n 
C18 H17 TW3 sing 404 n n 
C19 H18 TW3 sing 405 n n 
C20 H19 TW3 sing 406 n n 
C23 H20 TW3 sing 407 n n 
C25 H21 TW3 sing 408 n n 
C26 H22 TW3 sing 409 n n 
C3 H23 TW3 sing 410 n n 
C3 H24 TW3 sing 411 n n 
C3 H25 TW3 sing 412 n n 
C4 H26 TW3 sing 413 n n 
C6 H27 TW3 sing 414 n n 
C6 H28 TW3 sing 415 n n 
C7 H29 TW3 sing 416 n n 
C7 H30 TW3 sing 417 n n 
C9 H31 TW3 sing 418 n n 
C9 H32 TW3 sing 419 n n 
N1 H33 TW3 sing 420 n n 
N2 H34 TW3 sing 421 n n 
N5 H35 TW3 sing 422 n n 
N5 H36 TW3 sing 423 n n 
O10 H37 TW3 sing 424 n n 
O13 H38 TW3 sing 425 n n 
O15 H39 TW3 sing 426 n n 
O16 H40 TW3 sing 427 n n 
O4 H41 TW3 sing 428 n n 
O7 H42 TW3 sing 429 n n 
#
_atom_sites.entry_id                     8J99 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
M 3 TW3 B 1 801 801 TW3 COA . 
N 3 TW3 D 1 801 801 TW3 COA . 
O 3 TW3 G 1 801 801 TW3 COA . 
P 3 TW3 H 1 801 801 TW3 COA . 
Q 3 TW3 J 1 801 801 TW3 COA . 
R 3 TW3 L 1 801 801 TW3 COA . 
#
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 TW3 . . . N 3 196.562 209.055 176.801 1 119.33 ? C1 TW3 801 D 1 
HETATM 2 C C10 TW3 . . . N 3 201.889 217.056 182.524 1 119.33 ? C10 TW3 801 D 1 
HETATM 3 C C11 TW3 . . . N 3 201.66 218.001 184.762 1 119.33 ? C11 TW3 801 D 1 
HETATM 4 C C12 TW3 . . . N 3 201.94 217.89 186.257 1 119.33 ? C12 TW3 801 D 1 
HETATM 5 C C13 TW3 . . . N 3 201.335 216.651 186.922 1 119.33 ? C13 TW3 801 D 1 
HETATM 6 C C14 TW3 . . . N 3 199.874 216.519 186.498 1 119.33 ? C14 TW3 801 D 1 
HETATM 7 C C15 TW3 . . . N 3 202.093 215.397 186.486 1 119.33 ? C15 TW3 801 D 1 
HETATM 8 C C16 TW3 . . . N 3 201.401 216.773 188.444 1 119.33 ? C16 TW3 801 D 1 
HETATM 9 C C17 TW3 . . . N 3 206.92 215.768 188.204 1 119.33 ? C17 TW3 801 D 1 
HETATM 10 C C18 TW3 . . . N 3 207.398 216.483 186.969 1 119.33 ? C18 TW3 801 D 1 
HETATM 11 C C19 TW3 . . . N 3 207.803 215.9 184.798 1 119.33 ? C19 TW3 801 D 1 
HETATM 12 C C2 TW3 . . . N 3 197.311 209.625 175.635 1 119.33 ? C2 TW3 801 D 1 
HETATM 13 C C20 TW3 . . . N 3 208.318 214.523 182.748 1 119.33 ? C20 TW3 801 D 1 
HETATM 14 C C21 TW3 . . . N 3 206.388 213.826 182.188 1 119.33 ? C21 TW3 801 D 1 
HETATM 15 C C22 TW3 . . . N 3 205.248 213.242 181.611 1 119.33 ? C22 TW3 801 D 1 
HETATM 16 C C23 TW3 . . . N 3 204.035 214.235 183.309 1 119.33 ? C23 TW3 801 D 1 
HETATM 17 C C24 TW3 . . . N 3 206.204 214.592 183.321 1 119.33 ? C24 TW3 801 D 1 
HETATM 18 C C25 TW3 . . . N 3 209.033 215.463 185.574 1 119.33 ? C25 TW3 801 D 1 
HETATM 19 C C26 TW3 . . . N 3 208.91 216.465 186.717 1 119.33 ? C26 TW3 801 D 1 
HETATM 20 C C3 TW3 . . . N 3 196.932 209.008 174.325 1 119.33 ? C3 TW3 801 D 1 
HETATM 21 C C4 TW3 . . . N 3 198.229 210.595 175.714 1 119.33 ? C4 TW3 801 D 1 
HETATM 22 C C5 TW3 . . . N 3 198.758 211.317 176.887 1 119.33 ? C5 TW3 801 D 1 
HETATM 23 C C6 TW3 . . . N 3 200.101 213.14 178.43 1 119.33 ? C6 TW3 801 D 1 
HETATM 24 C C7 TW3 . . . N 3 200.947 214.39 178.623 1 119.33 ? C7 TW3 801 D 1 
HETATM 25 C C8 TW3 . . . N 3 200.776 215.799 180.632 1 119.33 ? C8 TW3 801 D 1 
HETATM 26 C C9 TW3 . . . N 3 201.014 215.894 182.124 1 119.33 ? C9 TW3 801 D 1 
HETATM 27 N N1 TW3 . . . N 3 201.167 214.674 180.033 1 119.33 ? N1 TW3 801 D 1 
HETATM 28 N N2 TW3 . . . N 3 202.157 217.068 183.955 1 119.33 ? N2 TW3 801 D 1 
HETATM 29 N N3 TW3 . . . N 3 207.452 215.037 183.679 1 119.33 ? N3 TW3 801 D 1 
HETATM 30 N N4 TW3 . . . N 3 207.728 213.793 181.835 1 119.33 ? N4 TW3 801 D 1 
HETATM 31 N N5 TW3 . . . N 3 205.278 212.489 180.515 1 119.33 ? N5 TW3 801 D 1 
HETATM 32 N N6 TW3 . . . N 3 204.058 213.473 182.209 1 119.33 ? N6 TW3 801 D 1 
HETATM 33 N N7 TW3 . . . N 3 205.038 214.836 183.938 1 119.33 ? N7 TW3 801 D 1 
HETATM 34 O O1 TW3 . . . N 3 198.429 211.043 178.018 1 119.33 ? O1 TW3 801 D 1 
HETATM 35 O O10 TW3 . . . N 3 207.103 218.038 190.079 1 119.33 -1 O10 TW3 801 D 1 
HETATM 36 O O11 TW3 . . . N 3 205.741 216.42 188.713 1 119.33 ? O11 TW3 801 D 1 
HETATM 37 O O12 TW3 . . . N 3 206.815 215.862 185.793 1 119.33 ? O12 TW3 801 D 1 
HETATM 38 O O13 TW3 . . . N 3 210.248 215.559 184.867 1 119.33 ? O13 TW3 801 D 1 
HETATM 39 O O14 TW3 . . . N 3 209.663 216.161 187.89 1 119.33 ? O14 TW3 801 D 1 
HETATM 40 O O15 TW3 . . . N 3 211.768 215.155 186.86 1 119.33 ? O15 TW3 801 D 1 
HETATM 41 O O16 TW3 . . . N 3 211.701 215.848 189.279 1 119.33 -1 O16 TW3 801 D 1 
HETATM 42 O O17 TW3 . . . N 3 211.667 217.598 187.466 1 119.33 ? O17 TW3 801 D 1 
HETATM 43 O O2 TW3 . . . N 3 200.239 216.714 180.014 1 119.33 ? O2 TW3 801 D 1 
HETATM 44 O O3 TW3 . . . N 3 200.981 218.935 184.347 1 119.33 ? O3 TW3 801 D 1 
HETATM 45 O O4 TW3 . . . N 3 203.33 217.998 186.508 1 119.33 ? O4 TW3 801 D 1 
HETATM 46 O O5 TW3 . . . N 3 202.754 216.996 188.878 1 119.33 ? O5 TW3 801 D 1 
HETATM 47 O O6 TW3 . . . N 3 202.869 219.499 188.873 1 119.33 -1 O6 TW3 801 D 1 
HETATM 48 O O7 TW3 . . . N 3 202.288 218.228 191.013 1 119.33 ? O7 TW3 801 D 1 
HETATM 49 O O8 TW3 . . . N 3 204.611 218.144 190.069 1 119.33 ? O8 TW3 801 D 1 
HETATM 50 O O9 TW3 . . . N 3 205.837 218.854 188.011 1 119.33 ? O9 TW3 801 D 1 
HETATM 51 P P1 TW3 . . . N 3 203.06 218.309 189.744 1 119.33 ? P1 TW3 801 D 1 
HETATM 52 P P2 TW3 . . . N 3 205.92 217.939 189.181 1 119.33 ? P2 TW3 801 D 1 
HETATM 53 P P3 TW3 . . . N 3 211.274 216.185 187.861 1 119.33 ? P3 TW3 801 D 1 
HETATM 54 S S1 TW3 . . . N 3 199.897 212.639 176.705 1 119.33 ? S1 TW3 801 D 1 
#
_model_server_stats.io_time_ms              128 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           54 
#