data_7YW3 # _model_server_result.job_id dcpmDpmhoewAgcCopyTb1g _model_server_result.datetime_utc '2024-11-26 05:27:28' _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 7yw3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7YW3 # _exptl.entry_id 7YW3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 639.296 _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] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate' _entity.pdbx_number_of_molecules 1 _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 7YW3 _cell.length_a 53.908 _cell.length_b 84.062 _cell.length_c 101.534 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YW3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H24 N5 O17 P3' _chem_comp.formula_weight 639.296 _chem_comp.id HQG _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] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-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 N1A C2A HQG doub 161 n y N1A C6A HQG sing 162 n y C2A N3A HQG sing 163 n y N6A C6A HQG sing 164 n n N3A C4A HQG doub 165 n y C6A C5A HQG doub 166 n y C4A C5A HQG sing 167 n y C4A N9A HQG sing 168 n y C5A N7A HQG sing 169 n y O4B C1B HQG sing 170 n n O4B C4B HQG sing 171 n n N9A C1B HQG sing 172 n n N9A C8A HQG sing 173 n y N7A C8A HQG doub 174 n y C1B C2B HQG sing 175 n n C4B C5B HQG sing 176 n n C4B C3B HQG sing 177 n n C5B O5B HQG sing 178 n n O3B C3B HQG sing 179 n n O5B PA HQG sing 180 n n C2B C3B HQG sing 181 n n C2B O2B HQG sing 182 n n O2A PA HQG doub 183 n n PA O1A HQG sing 184 n n PA O3 HQG sing 185 n n O3 PN HQG sing 186 n n O2N PN HQG doub 187 n n PN O1N HQG sing 188 n n PN O5D HQG sing 189 n n O5D C5D HQG sing 190 n n C5D C4D HQG sing 191 n n O4D C4D HQG sing 192 n n O4D C1D HQG sing 193 n n C4D C3D HQG sing 194 n n O1Z PZ HQG doub 195 n n C1D C2D HQG sing 196 n n C1D O4Z HQG sing 197 n n C2D C3D HQG sing 198 n n C2D O2D HQG sing 199 n n C3D O3D HQG sing 200 n n O4Z PZ HQG sing 201 n n PZ O2Z HQG sing 202 n n PZ O3Z HQG sing 203 n n C1B H1 HQG sing 204 n n C1D H2 HQG sing 205 n n C2A H3 HQG sing 206 n n C2B H4 HQG sing 207 n n C2D H5 HQG sing 208 n n C3B H6 HQG sing 209 n n C3D H7 HQG sing 210 n n C4B H8 HQG sing 211 n n C4D H9 HQG sing 212 n n C5B H10 HQG sing 213 n n C5B H11 HQG sing 214 n n C5D H12 HQG sing 215 n n C5D H13 HQG sing 216 n n C8A H14 HQG sing 217 n n N6A H15 HQG sing 218 n n N6A H16 HQG sing 219 n n O1A H17 HQG sing 220 n n O1N H18 HQG sing 221 n n O2B H19 HQG sing 222 n n O2D H20 HQG sing 223 n n O2Z H21 HQG sing 224 n n O3B H22 HQG sing 225 n n O3D H23 HQG sing 226 n n O3Z H24 HQG sing 227 n n # _atom_sites.entry_id 7YW3 _atom_sites.fract_transf_matrix[1][1] 0.01855 _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] 0.011896 _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] 0.009849 _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 B 2 HQG A 1 301 301 HQG HQG . C 3 EDO A 1 302 302 EDO EDO . D 4 HOH A 1 401 19 HOH HOH . D 4 HOH A 2 402 9 HOH HOH . D 4 HOH A 3 403 8 HOH HOH . D 4 HOH A 4 404 20 HOH HOH . D 4 HOH A 5 405 5 HOH HOH . D 4 HOH A 6 406 18 HOH HOH . D 4 HOH A 7 407 6 HOH HOH . D 4 HOH A 8 408 10 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 C1B HQG . . . B 2 -25.387 -21.98 -24.702 1 38.17 ? C1B HQG 301 A 1 HETATM 2 C C1D HQG . . . B 2 -21.382 -20.334 -14.433 0.19 41.67 ? C1D HQG 301 A 1 HETATM 3 C C2A HQG . . . B 2 -25.614 -22.985 -28.927 0.83 53.53 ? C2A HQG 301 A 1 HETATM 4 C C2B HQG . . . B 2 -25.793 -21.873 -23.441 0.21 42.59 ? C2B HQG 301 A 1 HETATM 5 C C2D HQG . . . B 2 -22.819 -19.811 -14.858 0 45.15 ? C2D HQG 301 A 1 HETATM 6 C C3B HQG . . . B 2 -24.677 -21.002 -22.838 1 39.02 ? C3B HQG 301 A 1 HETATM 7 C C3D HQG . . . B 2 -23.543 -20.793 -14.666 1 41.88 ? C3D HQG 301 A 1 HETATM 8 C C4A HQG . . . B 2 -25.96 -23.295 -26.642 0.78 37.22 ? C4A HQG 301 A 1 HETATM 9 C C4B HQG . . . B 2 -23.398 -21.735 -23.418 1 53.84 ? C4B HQG 301 A 1 HETATM 10 C C4D HQG . . . B 2 -22.594 -22.136 -14.971 0.37 36.24 ? C4D HQG 301 A 1 HETATM 11 C C5A HQG . . . B 2 -26.581 -24.454 -26.886 0.79 36.58 ? C5A HQG 301 A 1 HETATM 12 C C5B HQG . . . B 2 -23.149 -22.996 -22.582 0 41.04 ? C5B HQG 301 A 1 HETATM 13 C C5D HQG . . . B 2 -22.905 -22.689 -16.355 1 35.71 ? C5D HQG 301 A 1 HETATM 14 C C6A HQG . . . B 2 -26.722 -24.889 -28.184 0.93 36.57 ? C6A HQG 301 A 1 HETATM 15 C C8A HQG . . . B 2 -26.571 -24.139 -24.74 0.71 36.45 ? C8A HQG 301 A 1 HETATM 16 N N1A HQG . . . B 2 -26.244 -24.161 -29.178 0.9 37.04 ? N1A HQG 301 A 1 HETATM 17 N N3A HQG . . . B 2 -25.475 -22.555 -27.655 1 37.84 ? N3A HQG 301 A 1 HETATM 18 N N6A HQG . . . B 2 -27.345 -26.094 -28.717 0.73 36.22 ? N6A HQG 301 A 1 HETATM 19 N N7A HQG . . . B 2 -26.96 -24.976 -25.713 0.68 36.17 ? N7A HQG 301 A 1 HETATM 20 N N9A HQG . . . B 2 -25.954 -23.107 -25.319 0.36 37.23 ? N9A HQG 301 A 1 HETATM 21 O O1A HQG . . . B 2 -20.23 -22.585 -20.048 1 43.54 -1 O1A HQG 301 A 1 HETATM 22 O O1N HQG . . . B 2 -24.542 -22.696 -18.74 1 36.01 -1 O1N HQG 301 A 1 HETATM 23 O O1Z HQG . . . B 2 -19.057 -19.013 -13.631 1 57.7 ? O1Z HQG 301 A 1 HETATM 24 O O2A HQG . . . B 2 -22.207 -24.041 -19.73 0.95 34.3 ? O2A HQG 301 A 1 HETATM 25 O O2B HQG . . . B 2 -27.099 -21.191 -23.372 1 39.28 ? O2B HQG 301 A 1 HETATM 26 O O2D HQG . . . B 2 -23.248 -18.652 -13.99 0.88 52.1 ? O2D HQG 301 A 1 HETATM 27 O O2N HQG . . . B 2 -24.362 -20.23 -18.566 0.44 44.96 ? O2N HQG 301 A 1 HETATM 28 O O2Z HQG . . . B 2 -20.632 -18.075 -11.985 0.84 65.63 -1 O2Z HQG 301 A 1 HETATM 29 O O3 HQG . . . B 2 -22.597 -21.497 -19.987 0.91 46.24 ? O3 HQG 301 A 1 HETATM 30 O O3B HQG . . . B 2 -24.751 -19.762 -23.306 1 41.03 ? O3B HQG 301 A 1 HETATM 31 O O3D HQG . . . B 2 -23.99 -20.817 -13.258 0.38 45.54 ? O3D HQG 301 A 1 HETATM 32 O O3Z HQG . . . B 2 -19.355 -20.117 -11.444 0.64 45.85 -1 O3Z HQG 301 A 1 HETATM 33 O O4B HQG . . . B 2 -23.736 -22.087 -24.629 0.39 40.52 ? O4B HQG 301 A 1 HETATM 34 O O4D HQG . . . B 2 -21.372 -21.78 -14.906 1 52.71 ? O4D HQG 301 A 1 HETATM 35 O O4Z HQG . . . B 2 -21.255 -20.285 -13.167 0.24 48.98 ? O4Z HQG 301 A 1 HETATM 36 O O5B HQG . . . B 2 -21.82 -22.994 -22.077 0.9 46.38 ? O5B HQG 301 A 1 HETATM 37 O O5D HQG . . . B 2 -22.598 -21.699 -17.316 0.41 67.19 ? O5D HQG 301 A 1 HETATM 38 P PA HQG . . . B 2 -21.67 -22.812 -20.426 0.6 35.78 ? PA HQG 301 A 1 HETATM 39 P PN HQG . . . B 2 -23.587 -21.526 -18.652 0.89 37.61 ? PN HQG 301 A 1 HETATM 40 P PZ HQG . . . B 2 -20.05 -19.351 -12.542 1 41.2 ? PZ HQG 301 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 616 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #