data_5WS4 # _model_server_result.job_id TxIH8qf5DJMcU6DsHxwD-Q _model_server_result.datetime_utc '2025-04-19 12:55:48' _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 5ws4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":801}' # _entry.id 5WS4 # _exptl.entry_id 5WS4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.267 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE" _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 90 _cell.angle_gamma 90 _cell.entry_id 5WS4 _cell.length_a 229.652 _cell.length_b 229.652 _cell.length_c 154.584 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WS4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _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 _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 'C10 H15 N5 O9 P2 S' _chem_comp.formula_weight 443.267 _chem_comp.id AT4 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE 5'-O-(2-THIODIPHOSPHATE)" # 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 O5' PA AT4 sing 70 n n O5' C5' AT4 sing 71 n n C5' C4' AT4 sing 72 n n C5' "H5'1" AT4 sing 73 n n C5' "H5'2" AT4 sing 74 n n C4' C3' AT4 sing 75 n n C4' O4' AT4 sing 76 n n C4' H4' AT4 sing 77 n n O4' C1' AT4 sing 78 n n C3' O3' AT4 sing 79 n n C3' C2' AT4 sing 80 n n C3' H3' AT4 sing 81 n n O3' HO3' AT4 sing 82 n n C2' O2' AT4 sing 83 n n C2' C1' AT4 sing 84 n n C2' H2' AT4 sing 85 n n C1' N9 AT4 sing 86 n n C1' H1' AT4 sing 87 n n N1 C2 AT4 doub 88 n y N1 C6 AT4 sing 89 n y C2 N3 AT4 sing 90 n y C2 H2 AT4 sing 91 n n N3 C4 AT4 doub 92 n y C4 N9 AT4 sing 93 n y C4 C5 AT4 sing 94 n y C5 N7 AT4 sing 95 n y C5 C6 AT4 doub 96 n y C6 N6 AT4 sing 97 n n N6 HN61 AT4 sing 98 n n N6 HN62 AT4 sing 99 n n N7 C8 AT4 doub 100 n y C8 N9 AT4 sing 101 n y C8 H8 AT4 sing 102 n n O2' HO2' AT4 sing 103 n n PA O2A AT4 doub 104 n n PA O3A AT4 sing 105 n n PA O1A AT4 sing 106 n n O1A HO1A AT4 sing 107 n n O3A PB AT4 sing 108 n n PB S3B AT4 sing 109 n n PB O1B AT4 doub 110 n n PB O2B AT4 sing 111 n n O2B HO2B AT4 sing 112 n n S3B HS3B AT4 sing 113 n n # _atom_sites.entry_id 5WS4 _atom_sites.fract_transf_matrix[1][1] 0.004354 _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] 0.004354 _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] 0.006469 _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 AT4 A 1 801 801 AT4 AT4 . D 2 AT4 B 1 701 802 AT4 AT4 . # 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 O O5' AT4 . . . C 2 36.471 39.619 58.45 1 105.61 ? O5' AT4 801 A 1 HETATM 2 C C5' AT4 . . . C 2 36.721 40.604 59.405 1 111.99 ? C5' AT4 801 A 1 HETATM 3 C C4' AT4 . . . C 2 35.687 40.65 60.49 1 108.18 ? C4' AT4 801 A 1 HETATM 4 O O4' AT4 . . . C 2 36.233 41.015 61.603 1 110.47 ? O4' AT4 801 A 1 HETATM 5 C C3' AT4 . . . C 2 34.694 41.812 59.962 1 127.25 ? C3' AT4 801 A 1 HETATM 6 O O3' AT4 . . . C 2 33.33 41.268 59.907 1 142.13 ? O3' AT4 801 A 1 HETATM 7 C C2' AT4 . . . C 2 34.767 42.82 60.752 1 125.97 ? C2' AT4 801 A 1 HETATM 8 C C1' AT4 . . . C 2 35.752 42.437 61.9 1 119.55 ? C1' AT4 801 A 1 HETATM 9 N N1 AT4 . . . C 2 37.71 47.03 62.997 1 118.78 ? N1 AT4 801 A 1 HETATM 10 C C2 AT4 . . . C 2 36.441 46.645 63.204 1 113.23 ? C2 AT4 801 A 1 HETATM 11 N N3 AT4 . . . C 2 36.052 45.396 62.869 1 106.15 ? N3 AT4 801 A 1 HETATM 12 C C4 AT4 . . . C 2 36.937 44.545 62.329 1 106.38 ? C4 AT4 801 A 1 HETATM 13 C C5 AT4 . . . C 2 38.196 44.913 62.119 1 110.91 ? C5 AT4 801 A 1 HETATM 14 C C6 AT4 . . . C 2 38.593 46.187 62.461 1 117.23 ? C6 AT4 801 A 1 HETATM 15 N N6 AT4 . . . C 2 39.821 46.944 62.395 1 114.67 ? N6 AT4 801 A 1 HETATM 16 N N7 AT4 . . . C 2 38.848 43.873 61.576 1 105.65 ? N7 AT4 801 A 1 HETATM 17 C C8 AT4 . . . C 2 37.979 42.865 61.457 1 107.68 ? C8 AT4 801 A 1 HETATM 18 N N9 AT4 . . . C 2 36.805 43.285 61.919 1 109.41 ? N9 AT4 801 A 1 HETATM 19 O O2' AT4 . . . C 2 33.397 43.141 61.255 1 126.11 ? O2' AT4 801 A 1 HETATM 20 P PA AT4 . . . C 2 35.026 38.787 58.169 1 99.19 ? PA AT4 801 A 1 HETATM 21 O O2A AT4 . . . C 2 35.43 37.61 57.374 1 100.52 ? O2A AT4 801 A 1 HETATM 22 O O1A AT4 . . . C 2 34.314 38.297 59.41 1 100.87 ? O1A AT4 801 A 1 HETATM 23 O O3A AT4 . . . C 2 34.086 39.728 57.21 1 133.94 ? O3A AT4 801 A 1 HETATM 24 P PB AT4 . . . C 2 34.764 40.626 56.005 1 168.51 ? PB AT4 801 A 1 HETATM 25 O O1B AT4 . . . C 2 33.681 41.295 55.191 1 180.21 ? O1B AT4 801 A 1 HETATM 26 O O2B AT4 . . . C 2 35.682 41.722 56.615 1 166.94 ? O2B AT4 801 A 1 HETATM 27 S S3B AT4 . . . C 2 36.013 39.376 54.772 1 176.26 ? S3B AT4 801 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #