data_1V3Q # _model_server_result.job_id wdMQmi5XjZJW6hItpJNQ4A _model_server_result.datetime_utc '2024-11-13 09:43:43' _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 1v3q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":290}' # _entry.id 1V3Q # _exptl.entry_id 1V3Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 236.227 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-[(2R,5R)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE _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 120 _cell.entry_id 1V3Q _cell.length_a 141.33 _cell.length_b 141.33 _cell.length_c 161.45 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V3Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 70.665 122.39537 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -70.665 122.39537 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H12 N4 O3' _chem_comp.formula_weight 236.227 _chem_comp.id 2DI _chem_comp.mon_nstd_flag . _chem_comp.name 9-[(2R,5R)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2',3'-DIDEOXYINOSINE;Didanosine" # 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 N9 C4 2DI sing 1 n y N9 C8 2DI sing 2 n y N9 C1' 2DI sing 3 n n C4 N3 2DI sing 4 n n C4 C5 2DI doub 5 n y N3 C2 2DI doub 6 n n C2 N1 2DI sing 7 n n C2 H2 2DI sing 8 n n N1 C6 2DI sing 9 n n N1 HN1 2DI sing 10 n n C6 O6 2DI doub 11 n n C6 C5 2DI sing 12 n n C5 N7 2DI sing 13 n y N7 C8 2DI doub 14 n y C8 H8 2DI sing 15 n n C5' O5' 2DI sing 16 n n C5' C4' 2DI sing 17 n n C5' "H5'1" 2DI sing 18 n n C5' "H5'2" 2DI sing 19 n n O5' H5' 2DI sing 20 n n C4' O4' 2DI sing 21 n n C4' C3' 2DI sing 22 n n C4' H4' 2DI sing 23 n n O4' C1' 2DI sing 24 n n C1' C2' 2DI sing 25 n n C1' H1' 2DI sing 26 n n C2' C3' 2DI sing 27 n n C2' "H2'1" 2DI sing 28 n n C2' "H2'2" 2DI sing 29 n n C3' "H3'1" 2DI sing 30 n n C3' "H3'2" 2DI sing 31 n n # _atom_sites.entry_id 1V3Q _atom_sites.fract_transf_matrix[1][1] 0.007076 _atom_sites.fract_transf_matrix[1][2] 0.004085 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00817 _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] 0.006194 _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 SO4 E 1 291 291 SO4 SO4 . C 2 SO4 E 1 292 292 SO4 SO4 . D 2 SO4 E 1 293 293 SO4 SO4 . E 3 2DI E 1 290 290 2DI DDI . F 4 HOH E 1 294 294 HOH WAT . F 4 HOH E 2 295 295 HOH WAT . F 4 HOH E 3 296 296 HOH WAT . F 4 HOH E 4 297 297 HOH WAT . F 4 HOH E 5 298 298 HOH WAT . F 4 HOH E 6 299 299 HOH WAT . F 4 HOH E 7 300 300 HOH WAT . F 4 HOH E 8 301 301 HOH WAT . F 4 HOH E 9 302 302 HOH WAT . F 4 HOH E 10 303 303 HOH WAT . F 4 HOH E 11 304 304 HOH WAT . F 4 HOH E 12 305 305 HOH WAT . F 4 HOH E 13 306 306 HOH WAT . F 4 HOH E 14 307 307 HOH WAT . F 4 HOH E 15 308 308 HOH WAT . F 4 HOH E 16 309 309 HOH WAT . F 4 HOH E 17 310 310 HOH WAT . F 4 HOH E 18 311 311 HOH WAT . F 4 HOH E 19 312 312 HOH WAT . F 4 HOH E 20 313 313 HOH WAT . F 4 HOH E 21 314 314 HOH WAT . F 4 HOH E 22 315 315 HOH WAT . F 4 HOH E 23 316 316 HOH WAT . F 4 HOH E 24 317 317 HOH WAT . F 4 HOH E 25 318 318 HOH WAT . F 4 HOH E 26 319 319 HOH WAT . F 4 HOH E 27 320 320 HOH WAT . F 4 HOH E 28 321 321 HOH WAT . F 4 HOH E 29 322 322 HOH WAT . F 4 HOH E 30 323 323 HOH WAT . F 4 HOH E 31 324 324 HOH WAT . F 4 HOH E 32 325 325 HOH WAT . F 4 HOH E 33 326 326 HOH WAT . F 4 HOH E 34 327 327 HOH WAT . # 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 N N9 2DI . . . E 3 -16.959 88.498 0.94 1 35.76 ? N9 2DI 290 E 1 HETATM 2 C C4 2DI . . . E 3 -15.724 88.634 0.374 1 35.07 ? C4 2DI 290 E 1 HETATM 3 N N3 2DI . . . E 3 -14.511 88.231 0.835 1 31.6 ? N3 2DI 290 E 1 HETATM 4 C C2 2DI . . . E 3 -13.531 88.554 0.006 1 32.29 ? C2 2DI 290 E 1 HETATM 5 N N1 2DI . . . E 3 -13.723 89.219 -1.172 1 32.25 ? N1 2DI 290 E 1 HETATM 6 C C6 2DI . . . E 3 -14.947 89.643 -1.67 1 35.68 ? C6 2DI 290 E 1 HETATM 7 O O6 2DI . . . E 3 -15.001 90.25 -2.758 1 38.48 ? O6 2DI 290 E 1 HETATM 8 C C5 2DI . . . E 3 -16.005 89.301 -0.801 1 34.63 ? C5 2DI 290 E 1 HETATM 9 N N7 2DI . . . E 3 -17.345 89.541 -0.932 1 34.32 ? N7 2DI 290 E 1 HETATM 10 C C8 2DI . . . E 3 -17.939 89.035 0.172 1 33.15 ? C8 2DI 290 E 1 HETATM 11 C C5' 2DI . . . E 3 -18.481 90.631 3.878 1 38.48 ? C5' 2DI 290 E 1 HETATM 12 O O5' 2DI . . . E 3 -19.866 90.756 3.444 1 41.59 ? O5' 2DI 290 E 1 HETATM 13 C C4' 2DI . . . E 3 -18.259 89.156 4.15 1 37.95 ? C4' 2DI 290 E 1 HETATM 14 O O4' 2DI . . . E 3 -18.495 88.472 2.886 1 40.88 ? O4' 2DI 290 E 1 HETATM 15 C C1' 2DI . . . E 3 -17.283 87.842 2.315 1 37.23 ? C1' 2DI 290 E 1 HETATM 16 C C2' 2DI . . . E 3 -16.208 88.029 3.424 1 40.44 ? C2' 2DI 290 E 1 HETATM 17 C C3' 2DI . . . E 3 -16.854 88.811 4.63 1 41.38 ? C3' 2DI 290 E 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 17 #