data_8K5S
#
_model_server_result.job_id            RIchkP6tXYMpZeOlcoatEQ 
_model_server_result.datetime_utc      '2024-12-26 16:13:55' 
_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          8k5s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    8K5S 
#
_exptl.entry_id    8K5S 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              504.473 
_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]methyl ~{N}-(3-prop-2-ynoxyphenyl)carbonylsulfamate' 
_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          96.64 
_cell.angle_gamma         90 
_cell.entry_id            8K5S 
_cell.length_a            124.041 
_cell.length_b            57.649 
_cell.length_c            171.427 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K5S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 1 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_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 
_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           'C20 H20 N6 O8 S' 
_chem_comp.formula_weight    504.473 
_chem_comp.id                VPT 
_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]methyl ~{N}-(3-prop-2-ynoxyphenyl)carbonylsulfamate' 
_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
CBG OBF VPT sing 376 n n 
CBG CBH VPT sing 377 n n 
OBF CBB VPT sing 378 n n 
CBC CBB VPT doub 379 n y 
CBC CBD VPT sing 380 n y 
CBB CBA VPT sing 381 n y 
CBH CBI VPT trip 382 n n 
CBD CBE VPT doub 383 n y 
CBA CAY VPT doub 384 n y 
N6 C6 VPT sing 385 n n 
CBE CAY VPT sing 386 n y 
CAY CAX VPT sing 387 n n 
N7 C5 VPT sing 388 n y 
N7 C8 VPT doub 389 n y 
C6 C5 VPT sing 390 n y 
C6 N1 VPT doub 391 n y 
C5 C4 VPT doub 392 n y 
C8 N9 VPT sing 393 n y 
O13 C13 VPT sing 394 n n 
NAU CAX VPT sing 395 n n 
NAU SAT VPT sing 396 n n 
CAX OAZ VPT doub 397 n n 
C13 C12 VPT sing 398 n n 
C13 C14 VPT sing 399 n n 
N1 C2 VPT sing 400 n y 
C15 C14 VPT sing 401 n n 
C15 O15 VPT sing 402 n n 
C4 N9 VPT sing 403 n y 
C4 N3 VPT sing 404 n y 
N9 C11 VPT sing 405 n n 
OAW SAT VPT doub 406 n n 
C12 C11 VPT sing 407 n n 
C12 O12 VPT sing 408 n n 
C2 N3 VPT doub 409 n y 
C14 O14 VPT sing 410 n n 
SAT O15 VPT sing 411 n n 
SAT OAV VPT doub 412 n n 
C11 O14 VPT sing 413 n n 
C2 H1 VPT sing 414 n n 
CBI H2 VPT sing 415 n n 
CBG H3 VPT sing 416 n n 
CBG H4 VPT sing 417 n n 
CBA H5 VPT sing 418 n n 
CBC H6 VPT sing 419 n n 
CBD H7 VPT sing 420 n n 
CBE H8 VPT sing 421 n n 
NAU H9 VPT sing 422 n n 
C15 H10 VPT sing 423 n n 
C15 H11 VPT sing 424 n n 
C14 H12 VPT sing 425 n n 
C13 H13 VPT sing 426 n n 
O13 H14 VPT sing 427 n n 
C12 H15 VPT sing 428 n n 
O12 H16 VPT sing 429 n n 
C11 H17 VPT sing 430 n n 
C8 H18 VPT sing 431 n n 
N6 H19 VPT sing 432 n n 
N6 H20 VPT sing 433 n n 
#
_atom_sites.entry_id                     8K5S 
_atom_sites.fract_transf_matrix[1][1]    0.008062 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000939 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017346 
_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]    0.005873 
_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 VPT A 1 601 601 VPT 3PB . 
D 2 VPT B 1 601 601 VPT 3PB . 
E 3 HOH A 1 701 58 HOH HOH . 
E 3 HOH A 2 702 51 HOH HOH . 
E 3 HOH A 3 703 11 HOH HOH . 
E 3 HOH A 4 704 52 HOH HOH . 
E 3 HOH A 5 705 28 HOH HOH . 
E 3 HOH A 6 706 30 HOH HOH . 
E 3 HOH A 7 707 36 HOH HOH . 
E 3 HOH A 8 708 32 HOH HOH . 
E 3 HOH A 9 709 24 HOH HOH . 
E 3 HOH A 10 710 14 HOH HOH . 
E 3 HOH A 11 711 16 HOH HOH . 
E 3 HOH A 12 712 54 HOH HOH . 
E 3 HOH A 13 713 43 HOH HOH . 
E 3 HOH A 14 714 33 HOH HOH . 
E 3 HOH A 15 715 45 HOH HOH . 
E 3 HOH A 16 716 44 HOH HOH . 
E 3 HOH A 17 717 55 HOH HOH . 
E 3 HOH A 18 718 10 HOH HOH . 
E 3 HOH A 19 719 23 HOH HOH . 
E 3 HOH A 20 720 59 HOH HOH . 
E 3 HOH A 21 721 8 HOH HOH . 
E 3 HOH A 22 722 27 HOH HOH . 
E 3 HOH A 23 723 37 HOH HOH . 
E 3 HOH A 24 724 18 HOH HOH . 
E 3 HOH A 25 725 56 HOH HOH . 
E 3 HOH A 26 726 62 HOH HOH . 
E 3 HOH A 27 727 2 HOH HOH . 
E 3 HOH A 28 728 29 HOH HOH . 
E 3 HOH A 29 729 21 HOH HOH . 
E 3 HOH A 30 730 1 HOH HOH . 
E 3 HOH A 31 731 38 HOH HOH . 
E 3 HOH A 32 732 48 HOH HOH . 
E 3 HOH A 33 733 39 HOH HOH . 
E 3 HOH A 34 734 5 HOH HOH . 
E 3 HOH A 35 735 49 HOH HOH . 
F 3 HOH B 1 701 41 HOH HOH . 
F 3 HOH B 2 702 15 HOH HOH . 
F 3 HOH B 3 703 53 HOH HOH . 
F 3 HOH B 4 704 12 HOH HOH . 
F 3 HOH B 5 705 46 HOH HOH . 
F 3 HOH B 6 706 61 HOH HOH . 
F 3 HOH B 7 707 60 HOH HOH . 
F 3 HOH B 8 708 57 HOH HOH . 
F 3 HOH B 9 709 31 HOH HOH . 
F 3 HOH B 10 710 25 HOH HOH . 
F 3 HOH B 11 711 6 HOH HOH . 
F 3 HOH B 12 712 40 HOH HOH . 
F 3 HOH B 13 713 19 HOH HOH . 
F 3 HOH B 14 714 42 HOH HOH . 
F 3 HOH B 15 715 13 HOH HOH . 
F 3 HOH B 16 716 50 HOH HOH . 
F 3 HOH B 17 717 26 HOH HOH . 
F 3 HOH B 18 718 20 HOH HOH . 
F 3 HOH B 19 719 9 HOH HOH . 
F 3 HOH B 20 720 17 HOH HOH . 
F 3 HOH B 21 721 35 HOH HOH . 
F 3 HOH B 22 722 3 HOH HOH . 
F 3 HOH B 23 723 34 HOH HOH . 
F 3 HOH B 24 724 22 HOH HOH . 
F 3 HOH B 25 725 47 HOH HOH . 
F 3 HOH B 26 726 7 HOH HOH . 
F 3 HOH B 27 727 4 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 C2 VPT . . . D 2 -20.872 6.156 64.043 1 28.31 ? C2 VPT 601 B 1 
HETATM 2 C C4 VPT . . . D 2 -22.449 4.478 64.266 1 28.59 ? C4 VPT 601 B 1 
HETATM 3 C CBI VPT . . . D 2 -30.544 -2.081 67.408 1 52.04 ? CBI VPT 601 B 1 
HETATM 4 C CBH VPT . . . D 2 -30.348 -1.349 68.481 1 53.22 ? CBH VPT 601 B 1 
HETATM 5 C CBG VPT . . . D 2 -30.223 -0.585 69.635 1 48.51 ? CBG VPT 601 B 1 
HETATM 6 O OBF VPT . . . D 2 -29.644 0.786 69.387 1 44.04 ? OBF VPT 601 B 1 
HETATM 7 C CBB VPT . . . D 2 -29.055 1.443 68.295 1 32.18 ? CBB VPT 601 B 1 
HETATM 8 C CBA VPT . . . D 2 -28.504 0.831 67.183 1 28.32 ? CBA VPT 601 B 1 
HETATM 9 C CBC VPT . . . D 2 -29.001 2.828 68.372 1 29.96 ? CBC VPT 601 B 1 
HETATM 10 C CBD VPT . . . D 2 -28.429 3.566 67.347 1 28.97 ? CBD VPT 601 B 1 
HETATM 11 C CBE VPT . . . D 2 -27.875 2.945 66.236 1 26.39 ? CBE VPT 601 B 1 
HETATM 12 C CAY VPT . . . D 2 -27.911 1.573 66.143 1 28.04 ? CAY VPT 601 B 1 
HETATM 13 C CAX VPT . . . D 2 -27.36 0.944 64.979 1 31.39 ? CAX VPT 601 B 1 
HETATM 14 O OAZ VPT . . . D 2 -26.96 1.603 63.982 1 30.16 ? OAZ VPT 601 B 1 
HETATM 15 N NAU VPT . . . D 2 -27.395 -0.435 65.014 1 29.95 ? NAU VPT 601 B 1 
HETATM 16 S SAT VPT . . . D 2 -26.891 -1.288 63.792 1 27.01 ? SAT VPT 601 B 1 
HETATM 17 O OAV VPT . . . D 2 -27.739 -0.963 62.632 1 24.45 ? OAV VPT 601 B 1 
HETATM 18 O OAW VPT . . . D 2 -26.959 -2.763 64.235 1 22.95 ? OAW VPT 601 B 1 
HETATM 19 O O15 VPT . . . D 2 -25.513 -0.82 63.334 1 27.32 ? O15 VPT 601 B 1 
HETATM 20 C C15 VPT . . . D 2 -24.465 -0.813 64.234 1 27.61 ? C15 VPT 601 B 1 
HETATM 21 C C14 VPT . . . D 2 -23.352 0.026 63.574 1 27.65 ? C14 VPT 601 B 1 
HETATM 22 O O14 VPT . . . D 2 -23.743 1.368 63.126 1 25.83 ? O14 VPT 601 B 1 
HETATM 23 C C13 VPT . . . D 2 -22.262 0.306 64.643 1 26.7 ? C13 VPT 601 B 1 
HETATM 24 O O13 VPT . . . D 2 -21.506 -0.867 64.89 1 24.39 ? O13 VPT 601 B 1 
HETATM 25 C C12 VPT . . . D 2 -21.477 1.36 63.933 1 26.54 ? C12 VPT 601 B 1 
HETATM 26 O O12 VPT . . . D 2 -20.742 0.782 62.877 1 26.7 ? O12 VPT 601 B 1 
HETATM 27 C C11 VPT . . . D 2 -22.619 2.199 63.317 1 26.99 ? C11 VPT 601 B 1 
HETATM 28 N N9 VPT . . . D 2 -23.095 3.324 64.15 1 28.05 ? N9 VPT 601 B 1 
HETATM 29 C C8 VPT . . . D 2 -24.202 3.413 64.863 1 29.57 ? C8 VPT 601 B 1 
HETATM 30 N N7 VPT . . . D 2 -24.267 4.612 65.438 1 30.42 ? N7 VPT 601 B 1 
HETATM 31 C C5 VPT . . . D 2 -23.184 5.278 65.066 1 30.87 ? C5 VPT 601 B 1 
HETATM 32 N N3 VPT . . . D 2 -21.298 4.872 63.725 1 25.88 ? N3 VPT 601 B 1 
HETATM 33 N N1 VPT . . . D 2 -21.64 6.99 64.888 1 30.03 ? N1 VPT 601 B 1 
HETATM 34 C C6 VPT . . . D 2 -22.798 6.516 65.38 1 30.88 ? C6 VPT 601 B 1 
HETATM 35 N N6 VPT . . . D 2 -23.624 7.226 66.174 1 26.92 ? N6 VPT 601 B 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           35 
#