data_5M84
#
_model_server_result.job_id            1Irsz1iyCgVlLBjVm4gnlg 
_model_server_result.datetime_utc      '2025-02-05 06:52:58' 
_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          5m84 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    5M84 
#
_exptl.entry_id    5M84 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              817.533 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate' 
_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          95.84 
_cell.angle_gamma         90 
_cell.entry_id            5M84 
_cell.length_a            46.946 
_cell.length_b            59.763 
_cell.length_c            149.428 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M84 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,G 1 1 
B,F,H 2 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 F N N 
#
_chem_comp.formula           'C22 H32 N10 O16 P3 S 1' 
_chem_comp.formula_weight    817.533 
_chem_comp.id                YDZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate' 
_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
O11 P3 YDZ doub 389 n n 
O12 P3 YDZ sing 390 n n 
O12 C16 YDZ sing 391 n n 
P3 O9 YDZ sing 392 n n 
P3 O10 YDZ sing 393 n n 
O9 P2 YDZ sing 394 n n 
C16 C17 YDZ sing 395 n n 
C22 N7 YDZ sing 396 n n 
C18 O14 YDZ sing 397 n n 
C18 C19 YDZ sing 398 n n 
C18 C17 YDZ sing 399 n n 
O5 P1 YDZ doub 400 n n 
O7 P2 YDZ sing 401 n n 
O7 P1 YDZ sing 402 n n 
C20 O15 YDZ sing 403 n n 
C19 O15 YDZ sing 404 n n 
C19 C21 YDZ sing 405 n n 
C2 N7 YDZ doub 406 n y 
C2 N6 YDZ sing 407 n y 
C17 O13 YDZ sing 408 n n 
N7 C4 YDZ sing 409 n y 
P2 S1 YDZ sing 410 n n 
P2 O8 YDZ doub 411 n n 
P1 O6 YDZ sing 412 n n 
P1 O4 YDZ sing 413 n n 
N3 C7 YDZ doub 414 n y 
N3 C8 YDZ sing 415 n y 
O1 C11 YDZ sing 416 n n 
O1 C14 YDZ sing 417 n n 
C7 N2 YDZ sing 418 n y 
C11 N5 YDZ sing 419 n n 
C11 C12 YDZ sing 420 n n 
O2 C12 YDZ sing 421 n n 
N6 C21 YDZ sing 422 n n 
N6 C3 YDZ sing 423 n y 
O16 C5 YDZ sing 424 n n 
C4 C5 YDZ doub 425 n y 
C4 C3 YDZ sing 426 n y 
O13 C21 YDZ sing 427 n n 
C14 C13 YDZ sing 428 n n 
C14 C15 YDZ sing 429 n n 
C8 N5 YDZ sing 430 n y 
C8 C9 YDZ doub 431 n y 
N5 C10 YDZ sing 432 n y 
N2 C6 YDZ doub 433 n y 
O3 C13 YDZ sing 434 n n 
C5 N10 YDZ sing 435 n y 
C3 N8 YDZ doub 436 n y 
C12 C13 YDZ sing 437 n n 
O4 C15 YDZ sing 438 n n 
C9 C6 YDZ sing 439 n y 
C9 N4 YDZ sing 440 n y 
C6 N1 YDZ sing 441 n n 
C10 N4 YDZ doub 442 n y 
N10 C1 YDZ doub 443 n y 
N8 C1 YDZ sing 444 n y 
C1 N9 YDZ sing 445 n n 
C2 H1 YDZ sing 446 n n 
N1 H2 YDZ sing 447 n n 
N1 H3 YDZ sing 448 n n 
C7 H4 YDZ sing 449 n n 
C10 H5 YDZ sing 450 n n 
C11 H6 YDZ sing 451 n n 
C12 H7 YDZ sing 452 n n 
O2 H8 YDZ sing 453 n n 
C13 H9 YDZ sing 454 n n 
O3 H10 YDZ sing 455 n n 
C14 H11 YDZ sing 456 n n 
C15 H12 YDZ sing 457 n n 
C15 H13 YDZ sing 458 n n 
O6 H14 YDZ sing 459 n n 
S1 H15 YDZ sing 460 n n 
O10 H16 YDZ sing 461 n n 
C16 H17 YDZ sing 462 n n 
C16 H18 YDZ sing 463 n n 
C17 H19 YDZ sing 464 n n 
C18 H20 YDZ sing 465 n n 
O14 H21 YDZ sing 466 n n 
C19 H22 YDZ sing 467 n n 
C20 H23 YDZ sing 468 n n 
C20 H24 YDZ sing 469 n n 
C20 H25 YDZ sing 470 n n 
C21 H26 YDZ sing 471 n n 
C22 H27 YDZ sing 472 n n 
C22 H28 YDZ sing 473 n n 
C22 H29 YDZ sing 474 n n 
N9 H30 YDZ sing 475 n n 
N9 H31 YDZ sing 476 n n 
O16 H32 YDZ sing 477 n n 
#
_atom_sites.entry_id                     5M84 
_atom_sites.fract_transf_matrix[1][1]    0.021301 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002181 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016733 
_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]    0.006727 
_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 YDZ A 1 301 300 YDZ SSA . 
D 3 GOL A 1 302 1 GOL GOL . 
E 3 GOL A 1 303 2 GOL GOL . 
F 2 YDZ B 1 300 300 YDZ SSA . 
G 4 HOH A 1 401 68 HOH HOH . 
G 4 HOH A 2 402 18 HOH HOH . 
G 4 HOH A 3 403 1 HOH HOH . 
G 4 HOH A 4 404 54 HOH HOH . 
G 4 HOH A 5 405 130 HOH HOH . 
G 4 HOH A 6 406 15 HOH HOH . 
G 4 HOH A 7 407 78 HOH HOH . 
G 4 HOH A 8 408 96 HOH HOH . 
G 4 HOH A 9 409 25 HOH HOH . 
G 4 HOH A 10 410 86 HOH HOH . 
G 4 HOH A 11 411 101 HOH HOH . 
G 4 HOH A 12 412 8 HOH HOH . 
G 4 HOH A 13 413 51 HOH HOH . 
G 4 HOH A 14 414 9 HOH HOH . 
G 4 HOH A 15 415 22 HOH HOH . 
G 4 HOH A 16 416 12 HOH HOH . 
G 4 HOH A 17 417 27 HOH HOH . 
G 4 HOH A 18 418 33 HOH HOH . 
G 4 HOH A 19 419 103 HOH HOH . 
G 4 HOH A 20 420 23 HOH HOH . 
G 4 HOH A 21 421 40 HOH HOH . 
G 4 HOH A 22 422 67 HOH HOH . 
G 4 HOH A 23 423 110 HOH HOH . 
G 4 HOH A 24 424 28 HOH HOH . 
G 4 HOH A 25 425 109 HOH HOH . 
G 4 HOH A 26 426 3 HOH HOH . 
G 4 HOH A 27 427 16 HOH HOH . 
G 4 HOH A 28 428 170 HOH HOH . 
G 4 HOH A 29 429 14 HOH HOH . 
G 4 HOH A 30 430 108 HOH HOH . 
G 4 HOH A 31 431 11 HOH HOH . 
G 4 HOH A 32 432 32 HOH HOH . 
G 4 HOH A 33 433 62 HOH HOH . 
G 4 HOH A 34 434 88 HOH HOH . 
G 4 HOH A 35 435 31 HOH HOH . 
G 4 HOH A 36 436 45 HOH HOH . 
G 4 HOH A 37 437 7 HOH HOH . 
G 4 HOH A 38 438 102 HOH HOH . 
G 4 HOH A 39 439 5 HOH HOH . 
G 4 HOH A 40 440 47 HOH HOH . 
G 4 HOH A 41 441 172 HOH HOH . 
G 4 HOH A 42 442 4 HOH HOH . 
G 4 HOH A 43 443 53 HOH HOH . 
G 4 HOH A 44 444 71 HOH HOH . 
G 4 HOH A 45 445 20 HOH HOH . 
G 4 HOH A 46 446 131 HOH HOH . 
G 4 HOH A 47 447 2 HOH HOH . 
G 4 HOH A 48 448 99 HOH HOH . 
G 4 HOH A 49 449 179 HOH HOH . 
G 4 HOH A 50 450 35 HOH HOH . 
G 4 HOH A 51 451 90 HOH HOH . 
G 4 HOH A 52 452 19 HOH HOH . 
G 4 HOH A 53 453 116 HOH HOH . 
G 4 HOH A 54 454 120 HOH HOH . 
G 4 HOH A 55 455 147 HOH HOH . 
G 4 HOH A 56 456 161 HOH HOH . 
G 4 HOH A 57 457 89 HOH HOH . 
G 4 HOH A 58 458 30 HOH HOH . 
G 4 HOH A 59 459 183 HOH HOH . 
G 4 HOH A 60 460 91 HOH HOH . 
G 4 HOH A 61 461 168 HOH HOH . 
G 4 HOH A 62 462 26 HOH HOH . 
G 4 HOH A 63 463 41 HOH HOH . 
G 4 HOH A 64 464 159 HOH HOH . 
G 4 HOH A 65 465 84 HOH HOH . 
G 4 HOH A 66 466 177 HOH HOH . 
G 4 HOH A 67 467 160 HOH HOH . 
G 4 HOH A 68 468 49 HOH HOH . 
G 4 HOH A 69 469 66 HOH HOH . 
G 4 HOH A 70 470 10 HOH HOH . 
G 4 HOH A 71 471 69 HOH HOH . 
G 4 HOH A 72 472 122 HOH HOH . 
G 4 HOH A 73 473 57 HOH HOH . 
G 4 HOH A 74 474 21 HOH HOH . 
G 4 HOH A 75 475 114 HOH HOH . 
G 4 HOH A 76 476 80 HOH HOH . 
G 4 HOH A 77 477 140 HOH HOH . 
G 4 HOH A 78 478 95 HOH HOH . 
G 4 HOH A 79 479 184 HOH HOH . 
G 4 HOH A 80 480 119 HOH HOH . 
G 4 HOH A 81 481 52 HOH HOH . 
G 4 HOH A 82 482 17 HOH HOH . 
G 4 HOH A 83 483 143 HOH HOH . 
G 4 HOH A 84 484 87 HOH HOH . 
G 4 HOH A 85 485 167 HOH HOH . 
G 4 HOH A 86 486 107 HOH HOH . 
G 4 HOH A 87 487 173 HOH HOH . 
G 4 HOH A 88 488 39 HOH HOH . 
G 4 HOH A 89 489 97 HOH HOH . 
G 4 HOH A 90 490 171 HOH HOH . 
G 4 HOH A 91 491 37 HOH HOH . 
G 4 HOH A 92 492 42 HOH HOH . 
G 4 HOH A 93 493 138 HOH HOH . 
G 4 HOH A 94 494 169 HOH HOH . 
G 4 HOH A 95 495 163 HOH HOH . 
G 4 HOH A 96 496 151 HOH HOH . 
G 4 HOH A 97 497 121 HOH HOH . 
G 4 HOH A 98 498 155 HOH HOH . 
G 4 HOH A 99 499 63 HOH HOH . 
H 4 HOH B 1 401 145 HOH HOH . 
H 4 HOH B 2 402 48 HOH HOH . 
H 4 HOH B 3 403 61 HOH HOH . 
H 4 HOH B 4 404 38 HOH HOH . 
H 4 HOH B 5 405 158 HOH HOH . 
H 4 HOH B 6 406 76 HOH HOH . 
H 4 HOH B 7 407 113 HOH HOH . 
H 4 HOH B 8 408 64 HOH HOH . 
H 4 HOH B 9 409 106 HOH HOH . 
H 4 HOH B 10 410 34 HOH HOH . 
H 4 HOH B 11 411 176 HOH HOH . 
H 4 HOH B 12 412 60 HOH HOH . 
H 4 HOH B 13 413 58 HOH HOH . 
H 4 HOH B 14 414 125 HOH HOH . 
H 4 HOH B 15 415 59 HOH HOH . 
H 4 HOH B 16 416 6 HOH HOH . 
H 4 HOH B 17 417 127 HOH HOH . 
H 4 HOH B 18 418 70 HOH HOH . 
H 4 HOH B 19 419 13 HOH HOH . 
H 4 HOH B 20 420 46 HOH HOH . 
H 4 HOH B 21 421 79 HOH HOH . 
H 4 HOH B 22 422 85 HOH HOH . 
H 4 HOH B 23 423 44 HOH HOH . 
H 4 HOH B 24 424 24 HOH HOH . 
H 4 HOH B 25 425 92 HOH HOH . 
H 4 HOH B 26 426 175 HOH HOH . 
H 4 HOH B 27 427 98 HOH HOH . 
H 4 HOH B 28 428 135 HOH HOH . 
H 4 HOH B 29 429 77 HOH HOH . 
H 4 HOH B 30 430 93 HOH HOH . 
H 4 HOH B 31 431 82 HOH HOH . 
H 4 HOH B 32 432 136 HOH HOH . 
H 4 HOH B 33 433 128 HOH HOH . 
H 4 HOH B 34 434 182 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 YDZ . . . C 2 -102.843 14.019 61.151 1 50.71 ? C1 YDZ 301 A 1 
HETATM 2 C C2 YDZ . . . C 2 -98.696 15.45 60.381 1 40.67 ? C2 YDZ 301 A 1 
HETATM 3 C C3 YDZ . . . C 2 -100.821 15.107 60.742 1 46.27 ? C3 YDZ 301 A 1 
HETATM 4 C C4 YDZ . . . C 2 -100.158 13.901 60.752 1 39.03 ? C4 YDZ 301 A 1 
HETATM 5 C C5 YDZ . . . C 2 -100.872 12.721 60.971 1 37.31 ? C5 YDZ 301 A 1 
HETATM 6 O O4 YDZ . . . C 2 -93.771 22.623 58.021 1 86.13 ? O4 YDZ 301 A 1 
HETATM 7 P P1 YDZ . . . C 2 -93.304 22.009 59.436 1 83.18 ? P1 YDZ 301 A 1 
HETATM 8 O O5 YDZ . . . C 2 -93.972 22.742 60.579 1 85.55 ? O5 YDZ 301 A 1 
HETATM 9 O O6 YDZ . . . C 2 -91.802 22.122 59.564 1 82.32 ? O6 YDZ 301 A 1 
HETATM 10 O O7 YDZ . . . C 2 -93.758 20.469 59.489 1 74.93 ? O7 YDZ 301 A 1 
HETATM 11 P P2 YDZ . . . C 2 -92.979 19.416 60.424 1 62.46 ? P2 YDZ 301 A 1 
HETATM 12 O O8 YDZ . . . C 2 -92.327 20.084 61.57 1 74.3 ? O8 YDZ 301 A 1 
HETATM 13 S S1 YDZ . . . C 2 -91.583 18.41 59.267 1 61.63 ? S1 YDZ 301 A 1 
HETATM 14 O O9 YDZ . . . C 2 -94.074 18.409 61.025 1 56.53 ? O9 YDZ 301 A 1 
HETATM 15 P P3 YDZ . . . C 2 -95.124 17.615 60.105 1 46.86 ? P3 YDZ 301 A 1 
HETATM 16 O O10 YDZ . . . C 2 -95.181 18.114 58.694 1 35.62 ? O10 YDZ 301 A 1 
HETATM 17 O O11 YDZ . . . C 2 -94.839 16.137 60.196 1 52.65 ? O11 YDZ 301 A 1 
HETATM 18 O O12 YDZ . . . C 2 -96.569 17.91 60.751 1 51.14 ? O12 YDZ 301 A 1 
HETATM 19 C C16 YDZ . . . C 2 -97.119 19.205 60.6 1 46.71 ? C16 YDZ 301 A 1 
HETATM 20 C C17 YDZ . . . C 2 -98.607 19.08 60.838 1 52.67 ? C17 YDZ 301 A 1 
HETATM 21 O O13 YDZ . . . C 2 -99.176 18.22 59.852 1 51.12 ? O13 YDZ 301 A 1 
HETATM 22 C C18 YDZ . . . C 2 -98.922 18.418 62.163 1 52.32 ? C18 YDZ 301 A 1 
HETATM 23 O O14 YDZ . . . C 2 -98.866 19.37 63.228 1 53.72 ? O14 YDZ 301 A 1 
HETATM 24 C C19 YDZ . . . C 2 -100.317 17.896 61.902 1 53.76 ? C19 YDZ 301 A 1 
HETATM 25 O O15 YDZ . . . C 2 -101.297 18.923 62.055 1 56.57 ? O15 YDZ 301 A 1 
HETATM 26 C C20 YDZ . . . C 2 -102.57 18.392 62.429 1 53.97 ? C20 YDZ 301 A 1 
HETATM 27 C C21 YDZ . . . C 2 -100.238 17.475 60.441 1 48.71 ? C21 YDZ 301 A 1 
HETATM 28 N N6 YDZ . . . C 2 -99.91 16.044 60.495 1 42.97 ? N6 YDZ 301 A 1 
HETATM 29 N N7 YDZ . . . C 2 -98.847 14.122 60.535 1 39.06 ? N7 YDZ 301 A 1 
HETATM 30 C C22 YDZ . . . C 2 -97.732 13.133 60.471 1 36.38 ? C22 YDZ 301 A 1 
HETATM 31 N N8 YDZ . . . C 2 -102.157 15.161 60.93 1 43.21 ? N8 YDZ 301 A 1 
HETATM 32 N N9 YDZ . . . C 2 -104.183 14.094 61.347 1 50.15 ? N9 YDZ 301 A 1 
HETATM 33 N N10 YDZ . . . C 2 -102.211 12.82 61.176 1 43.3 ? N10 YDZ 301 A 1 
HETATM 34 O O16 YDZ . . . C 2 -100.297 11.49 61 1 33.66 ? O16 YDZ 301 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           34 
#