data_8JXM
#
_model_server_result.job_id            0NxLtilJW58bEnXdxfEVkw 
_model_server_result.datetime_utc      '2024-10-10 02:31:55' 
_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          8jxm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":601}' 
#
_entry.id    8JXM 
#
_exptl.entry_id    8JXM 
_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    12-meric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X 
_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
? 3 M N N 
? 3 N N N 
? 3 P N N 
? 3 T N N 
? 3 W N N 
? 3 X 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 364 n n 
O7 P1 TW3 sing 365 n n 
P1 O8 TW3 sing 366 n n 
P1 O5 TW3 sing 367 n n 
O8 P2 TW3 sing 368 n n 
O9 P2 TW3 doub 369 n n 
O17 P3 TW3 doub 370 n n 
O11 P2 TW3 sing 371 n n 
O11 C17 TW3 sing 372 n n 
P2 O10 TW3 sing 373 n n 
O5 C16 TW3 sing 374 n n 
C17 C18 TW3 sing 375 n n 
C16 C13 TW3 sing 376 n n 
O14 P3 TW3 sing 377 n n 
O14 C26 TW3 sing 378 n n 
P3 O15 TW3 sing 379 n n 
P3 O16 TW3 sing 380 n n 
C18 C26 TW3 sing 381 n n 
C18 O12 TW3 sing 382 n n 
C26 C25 TW3 sing 383 n n 
C13 C14 TW3 sing 384 n n 
C13 C15 TW3 sing 385 n n 
C13 C12 TW3 sing 386 n n 
O4 C12 TW3 sing 387 n n 
O12 C19 TW3 sing 388 n n 
C12 C11 TW3 sing 389 n n 
C25 O13 TW3 sing 390 n n 
C25 C19 TW3 sing 391 n n 
C19 N3 TW3 sing 392 n n 
C11 O3 TW3 doub 393 n n 
C11 N2 TW3 sing 394 n n 
N7 C24 TW3 doub 395 n y 
N7 C23 TW3 sing 396 n y 
N3 C24 TW3 sing 397 n y 
N3 C20 TW3 sing 398 n y 
N2 C10 TW3 sing 399 n n 
C24 C21 TW3 sing 400 n y 
C23 N6 TW3 doub 401 n y 
C20 N4 TW3 doub 402 n y 
C21 N4 TW3 sing 403 n y 
C21 C22 TW3 doub 404 n y 
N6 C22 TW3 sing 405 n y 
C10 C9 TW3 sing 406 n n 
C22 N5 TW3 sing 407 n n 
C9 C8 TW3 sing 408 n n 
C8 N1 TW3 sing 409 n n 
C8 O2 TW3 doub 410 n n 
N1 C7 TW3 sing 411 n n 
C7 C6 TW3 sing 412 n n 
S1 C6 TW3 sing 413 n n 
S1 C5 TW3 sing 414 n n 
C4 C5 TW3 sing 415 n n 
C4 C2 TW3 doub 416 n n 
C5 O1 TW3 doub 417 n n 
C1 C2 TW3 sing 418 n n 
C2 C3 TW3 sing 419 n n 
C1 H1 TW3 sing 420 n n 
C1 H2 TW3 sing 421 n n 
C1 H3 TW3 sing 422 n n 
C10 H4 TW3 sing 423 n n 
C10 H5 TW3 sing 424 n n 
C12 H6 TW3 sing 425 n n 
C14 H7 TW3 sing 426 n n 
C14 H8 TW3 sing 427 n n 
C14 H9 TW3 sing 428 n n 
C15 H10 TW3 sing 429 n n 
C15 H11 TW3 sing 430 n n 
C15 H12 TW3 sing 431 n n 
C16 H13 TW3 sing 432 n n 
C16 H14 TW3 sing 433 n n 
C17 H15 TW3 sing 434 n n 
C17 H16 TW3 sing 435 n n 
C18 H17 TW3 sing 436 n n 
C19 H18 TW3 sing 437 n n 
C20 H19 TW3 sing 438 n n 
C23 H20 TW3 sing 439 n n 
C25 H21 TW3 sing 440 n n 
C26 H22 TW3 sing 441 n n 
C3 H23 TW3 sing 442 n n 
C3 H24 TW3 sing 443 n n 
C3 H25 TW3 sing 444 n n 
C4 H26 TW3 sing 445 n n 
C6 H27 TW3 sing 446 n n 
C6 H28 TW3 sing 447 n n 
C7 H29 TW3 sing 448 n n 
C7 H30 TW3 sing 449 n n 
C9 H31 TW3 sing 450 n n 
C9 H32 TW3 sing 451 n n 
N1 H33 TW3 sing 452 n n 
N2 H34 TW3 sing 453 n n 
N5 H35 TW3 sing 454 n n 
N5 H36 TW3 sing 455 n n 
O10 H37 TW3 sing 456 n n 
O13 H38 TW3 sing 457 n n 
O15 H39 TW3 sing 458 n n 
O16 H40 TW3 sing 459 n n 
O4 H41 TW3 sing 460 n n 
O7 H42 TW3 sing 461 n n 
#
_atom_sites.entry_id                     8JXM 
_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 K 1 601 601 TW3 COA . 
N 3 TW3 A 1 601 601 TW3 COA . 
O 4 BTI C 1 601 800 BTI BTI . 
P 3 TW3 C 1 602 601 TW3 COA . 
Q 4 BTI F 1 801 801 BTI BTI . 
R 4 BTI G 1 801 801 BTI BTI . 
S 4 BTI H 1 601 800 BTI BTI . 
T 3 TW3 H 1 602 603 TW3 COA . 
U 4 BTI I 1 801 801 BTI BTI . 
V 4 BTI M 1 801 801 BTI BTI . 
W 3 TW3 E 1 601 604 TW3 COA . 
X 3 TW3 J 1 601 602 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 . . . X 3 189.888 164.519 135.86 1 107.89 ? C1 TW3 601 J 1 
HETATM 2 C C10 TW3 . . . X 3 192.241 157.163 127.851 1 106.56 ? C10 TW3 601 J 1 
HETATM 3 C C11 TW3 . . . X 3 192.112 154.724 127.688 1 107.53 ? C11 TW3 601 J 1 
HETATM 4 C C12 TW3 . . . X 3 191.241 153.487 127.494 1 107.61 ? C12 TW3 601 J 1 
HETATM 5 C C13 TW3 . . . X 3 190.158 153.308 128.567 1 107.42 ? C13 TW3 601 J 1 
HETATM 6 C C14 TW3 . . . X 3 190.799 153.429 129.951 1 107.68 ? C14 TW3 601 J 1 
HETATM 7 C C15 TW3 . . . X 3 189.096 154.4 128.423 1 107.64 ? C15 TW3 601 J 1 
HETATM 8 C C16 TW3 . . . X 3 189.484 151.939 128.455 1 107.63 ? C16 TW3 601 J 1 
HETATM 9 C C17 TW3 . . . X 3 186.507 153.719 123.999 1 108.27 ? C17 TW3 601 J 1 
HETATM 10 C C18 TW3 . . . X 3 187.419 154.576 123.16 1 108.53 ? C18 TW3 601 J 1 
HETATM 11 C C19 TW3 . . . X 3 187.585 156.879 123.172 1 107.74 ? C19 TW3 601 J 1 
HETATM 12 C C2 TW3 . . . X 3 190.801 165.446 135.115 1 110.37 ? C2 TW3 601 J 1 
HETATM 13 C C20 TW3 . . . X 3 186.852 159.239 123.693 1 107.44 ? C20 TW3 601 J 1 
HETATM 14 C C21 TW3 . . . X 3 187.662 159.536 125.64 1 106.78 ? C21 TW3 601 J 1 
HETATM 15 C C22 TW3 . . . X 3 188.083 159.984 126.906 1 107.18 ? C22 TW3 601 J 1 
HETATM 16 C C23 TW3 . . . X 3 189.061 157.905 127.178 1 107.92 ? C23 TW3 601 J 1 
HETATM 17 C C24 TW3 . . . X 3 188.016 158.252 125.27 1 106.98 ? C24 TW3 601 J 1 
HETATM 18 C C25 TW3 . . . X 3 186.304 156.518 122.434 1 108.37 ? C25 TW3 601 J 1 
HETATM 19 C C26 TW3 . . . X 3 186.792 155.179 121.899 1 108.59 ? C26 TW3 601 J 1 
HETATM 20 C C3 TW3 . . . X 3 191.053 166.741 135.825 1 107.49 ? C3 TW3 601 J 1 
HETATM 21 C C4 TW3 . . . X 3 191.351 165.163 133.931 1 111.45 ? C4 TW3 601 J 1 
HETATM 22 C C5 TW3 . . . X 3 191.193 163.937 133.124 1 111.38 ? C5 TW3 601 J 1 
HETATM 23 C C6 TW3 . . . X 3 191.509 162.078 131.12 1 108.22 ? C6 TW3 601 J 1 
HETATM 24 C C7 TW3 . . . X 3 192.144 161.57 129.835 1 107.39 ? C7 TW3 601 J 1 
HETATM 25 C C8 TW3 . . . X 3 192.45 159.17 129.383 1 107.15 ? C8 TW3 601 J 1 
HETATM 26 C C9 TW3 . . . X 3 191.769 157.845 129.116 1 107.31 ? C9 TW3 601 J 1 
HETATM 27 N N1 TW3 . . . X 3 191.662 160.24 129.486 1 107.42 ? N1 TW3 601 J 1 
HETATM 28 N N2 TW3 . . . X 3 191.527 155.918 127.609 1 106.86 ? N2 TW3 601 J 1 
HETATM 29 N N3 TW3 . . . X 3 187.489 158.067 124.014 1 107.4 ? N3 TW3 601 J 1 
HETATM 30 N N4 TW3 . . . X 3 186.931 160.149 124.632 1 106.62 ? N4 TW3 601 J 1 
HETATM 31 N N5 TW3 . . . X 3 187.819 161.198 127.388 1 107.01 ? N5 TW3 601 J 1 
HETATM 32 N N6 TW3 . . . X 3 188.798 159.123 127.668 1 107.82 ? N6 TW3 601 J 1 
HETATM 33 N N7 TW3 . . . X 3 188.721 157.377 126.005 1 107.22 ? N7 TW3 601 J 1 
HETATM 34 O O1 TW3 . . . X 3 190.482 163.026 133.482 1 109.89 ? O1 TW3 601 J 1 
HETATM 35 O O10 TW3 . . . X 3 187.26 151.073 122.842 1 111.05 ? O10 TW3 601 J 1 
HETATM 36 O O11 TW3 . . . X 3 187.287 152.75 124.721 1 109.47 ? O11 TW3 601 J 1 
HETATM 37 O O12 TW3 . . . X 3 187.832 155.729 123.944 1 107.63 ? O12 TW3 601 J 1 
HETATM 38 O O13 TW3 . . . X 3 185.92 157.44 121.438 1 109.54 ? O13 TW3 601 J 1 
HETATM 39 O O14 TW3 . . . X 3 185.809 154.328 121.309 1 109.56 ? O14 TW3 601 J 1 
HETATM 40 O O15 TW3 . . . X 3 184.218 156.063 120.411 1 110.16 ? O15 TW3 601 J 1 
HETATM 41 O O16 TW3 . . . X 3 184.067 153.674 119.626 1 110.2 ? O16 TW3 601 J 1 
HETATM 42 O O17 TW3 . . . X 3 186.024 155.109 118.933 1 109.79 ? O17 TW3 601 J 1 
HETATM 43 O O2 TW3 . . . X 3 193.67 159.244 129.511 1 107.16 ? O2 TW3 601 J 1 
HETATM 44 O O3 TW3 . . . X 3 193.312 154.59 127.915 1 108.06 ? O3 TW3 601 J 1 
HETATM 45 O O4 TW3 . . . X 3 190.698 153.488 126.186 1 107.79 ? O4 TW3 601 J 1 
HETATM 46 O O5 TW3 . . . X 3 188.92 151.742 127.142 1 107.96 ? O5 TW3 601 J 1 
HETATM 47 O O6 TW3 . . . X 3 190.939 151.105 125.778 1 109.54 ? O6 TW3 601 J 1 
HETATM 48 O O7 TW3 . . . X 3 189.469 149.316 126.853 1 108.43 ? O7 TW3 601 J 1 
HETATM 49 O O8 TW3 . . . X 3 188.615 150.662 124.909 1 109.52 ? O8 TW3 601 J 1 
HETATM 50 O O9 TW3 . . . X 3 189.362 152.443 123.3 1 109.76 ? O9 TW3 601 J 1 
HETATM 51 P P1 TW3 . . . X 3 189.584 150.642 126.184 1 109.4 ? P1 TW3 601 J 1 
HETATM 52 P P2 TW3 . . . X 3 188.154 151.747 123.824 1 111.01 ? P2 TW3 601 J 1 
HETATM 53 P P3 TW3 . . . X 3 184.99 154.818 120.01 1 112.1 ? P3 TW3 601 J 1 
HETATM 54 S S1 TW3 . . . X 3 192.04 163.739 131.598 1 111.79 ? S1 TW3 601 J 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    337 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           54 
#