data_8K5S # _model_server_result.job_id 4S9XeTBpLhlijW5H0a5Z8Q _model_server_result.datetime_utc '2024-12-05 13:14:20' _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":"C","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 . . . C 2 11.596 8.079 20.584 1 27.99 ? C2 VPT 601 A 1 HETATM 2 C C4 VPT . . . C 2 13.168 6.367 20.24 1 27.51 ? C4 VPT 601 A 1 HETATM 3 C CBI VPT . . . C 2 21.351 0.156 17.61 1 44.21 ? CBI VPT 601 A 1 HETATM 4 C CBH VPT . . . C 2 21.121 0.68 16.63 1 39.91 ? CBH VPT 601 A 1 HETATM 5 C CBG VPT . . . C 2 20.933 1.208 15.51 1 38.35 ? CBG VPT 601 A 1 HETATM 6 O OBF VPT . . . C 2 20.689 2.656 15.597 1 36.63 ? OBF VPT 601 A 1 HETATM 7 C CBB VPT . . . C 2 20.023 3.375 16.562 1 29.57 ? CBB VPT 601 A 1 HETATM 8 C CBA VPT . . . C 2 19.363 2.739 17.595 1 27.14 ? CBA VPT 601 A 1 HETATM 9 C CBC VPT . . . C 2 20.042 4.789 16.472 1 27.49 ? CBC VPT 601 A 1 HETATM 10 C CBD VPT . . . C 2 19.43 5.584 17.423 1 25.39 ? CBD VPT 601 A 1 HETATM 11 C CBE VPT . . . C 2 18.784 4.912 18.462 1 27.8 ? CBE VPT 601 A 1 HETATM 12 C CAY VPT . . . C 2 18.72 3.5 18.566 1 26.27 ? CAY VPT 601 A 1 HETATM 13 C CAX VPT . . . C 2 18.082 2.864 19.652 1 24.94 ? CAX VPT 601 A 1 HETATM 14 O OAZ VPT . . . C 2 17.608 3.532 20.582 1 23.35 ? OAZ VPT 601 A 1 HETATM 15 N NAU VPT . . . C 2 18.132 1.504 19.63 1 25.41 ? NAU VPT 601 A 1 HETATM 16 S SAT VPT . . . C 2 17.58 0.602 20.854 1 25.28 ? SAT VPT 601 A 1 HETATM 17 O OAV VPT . . . C 2 18.385 0.96 22.079 1 24.63 ? OAV VPT 601 A 1 HETATM 18 O OAW VPT . . . C 2 17.753 -0.875 20.444 1 24.25 ? OAW VPT 601 A 1 HETATM 19 O O15 VPT . . . C 2 16.094 0.909 21.164 1 26.81 ? O15 VPT 601 A 1 HETATM 20 C C15 VPT . . . C 2 15.118 0.981 20.144 1 25.54 ? C15 VPT 601 A 1 HETATM 21 C C14 VPT . . . C 2 14.027 1.83 20.762 1 26.11 ? C14 VPT 601 A 1 HETATM 22 O O14 VPT . . . C 2 14.481 3.178 21.247 1 25.46 ? O14 VPT 601 A 1 HETATM 23 C C13 VPT . . . C 2 12.906 2.118 19.732 1 24.97 ? C13 VPT 601 A 1 HETATM 24 O O13 VPT . . . C 2 12.1 0.925 19.605 1 23.82 ? O13 VPT 601 A 1 HETATM 25 C C12 VPT . . . C 2 12.19 3.208 20.467 1 23.22 ? C12 VPT 601 A 1 HETATM 26 O O12 VPT . . . C 2 11.496 2.539 21.54 1 22.45 ? O12 VPT 601 A 1 HETATM 27 C C11 VPT . . . C 2 13.328 4.049 21.09 1 23.73 ? C11 VPT 601 A 1 HETATM 28 N N9 VPT . . . C 2 13.8 5.195 20.312 1 25.14 ? N9 VPT 601 A 1 HETATM 29 C C8 VPT . . . C 2 14.922 5.266 19.587 1 24.98 ? C8 VPT 601 A 1 HETATM 30 N N7 VPT . . . C 2 15.003 6.464 19.052 1 26.43 ? N7 VPT 601 A 1 HETATM 31 C C5 VPT . . . C 2 13.912 7.17 19.435 1 29.04 ? C5 VPT 601 A 1 HETATM 32 N N3 VPT . . . C 2 12.014 6.782 20.817 1 27.21 ? N3 VPT 601 A 1 HETATM 33 N N1 VPT . . . C 2 12.375 8.921 19.75 1 29.02 ? N1 VPT 601 A 1 HETATM 34 C C6 VPT . . . C 2 13.517 8.446 19.185 1 29.33 ? C6 VPT 601 A 1 HETATM 35 N N6 VPT . . . C 2 14.302 9.224 18.386 1 28.72 ? N6 VPT 601 A 1 # _model_server_stats.io_time_ms 118 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 381 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #