data_4DAR # _model_server_result.job_id WbOtFyKasCx-m5Mar8DNNg _model_server_result.datetime_utc '2024-11-25 01:51:22' _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 4dar # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4DAR # _exptl.entry_id 4DAR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 266.253 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL" _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 4DAR _cell.length_a 135.638 _cell.length_b 135.638 _cell.length_c 57.56 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DAR _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 135.638 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 67.819 117.465954 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 67.819 117.465954 28.78 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 135.638 0 28.78 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 28.78 # _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 'C11 H14 N4 O4' _chem_comp.formula_weight 266.253 _chem_comp.id TBN _chem_comp.mon_nstd_flag n _chem_comp.name "'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 7-DEAZAADENOSINE # 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' C5' TBN sing 288 n n O5' H5' TBN sing 289 n n C5' C4' TBN sing 290 n n C5' "H5'1" TBN sing 291 n n C5' "H5'2" TBN sing 292 n n C4' O4' TBN sing 293 n n C4' C3' TBN sing 294 n n C4' H4' TBN sing 295 n n O4' C1' TBN sing 296 n n C1' N9 TBN sing 297 n n C1' C2' TBN sing 298 n n C1' H1' TBN sing 299 n n N9 C8 TBN sing 300 n y N9 C4 TBN sing 301 n y C8 C7 TBN doub 302 n y C8 H8 TBN sing 303 n n C7 C5 TBN sing 304 n y C7 H7 TBN sing 305 n n C5 C6 TBN doub 306 n y C5 C4 TBN sing 307 n y C6 N1 TBN sing 308 n y C6 N6 TBN sing 309 n n N1 C2 TBN doub 310 n y C2 N3 TBN sing 311 n y C2 H2 TBN sing 312 n n N3 C4 TBN doub 313 n y N6 HN61 TBN sing 314 n n N6 HN62 TBN sing 315 n n C2' O2' TBN sing 316 n n C2' C3' TBN sing 317 n n C2' H2' TBN sing 318 n n O2' H1 TBN sing 319 n n C3' O3' TBN sing 320 n n C3' H3' TBN sing 321 n n O3' H3 TBN sing 322 n n # _atom_sites.entry_id 4DAR _atom_sites.fract_transf_matrix[1][1] 0.007373 _atom_sites.fract_transf_matrix[1][2] 0.004257 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008513 _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] 0.017373 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id TBN _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id TBN _pdbx_nonpoly_scheme.auth_mon_id TBN _pdbx_nonpoly_scheme.pdb_ins_code . # 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' TBN . . . B 2 42.229 30.287 23.742 1 55.1 ? O5' TBN 301 A 1 HETATM 2 C C5' TBN . . . B 2 42.857 30.458 22.462 1 54.7 ? C5' TBN 301 A 1 HETATM 3 C C4' TBN . . . B 2 42.112 31.498 21.631 1 54.22 ? C4' TBN 301 A 1 HETATM 4 O O4' TBN . . . B 2 41.338 32.351 22.48 1 54.76 ? O4' TBN 301 A 1 HETATM 5 C C1' TBN . . . B 2 41.797 33.709 22.484 1 55.32 ? C1' TBN 301 A 1 HETATM 6 N N9 TBN . . . B 2 42.256 33.975 23.88 1 57.21 ? N9 TBN 301 A 1 HETATM 7 C C8 TBN . . . B 2 41.332 34.139 24.866 1 57.75 ? C8 TBN 301 A 1 HETATM 8 C C7 TBN . . . B 2 41.987 34.342 26.051 1 58.11 ? C7 TBN 301 A 1 HETATM 9 C C5 TBN . . . B 2 43.369 34.282 25.752 1 58.67 ? C5 TBN 301 A 1 HETATM 10 C C6 TBN . . . B 2 44.498 34.408 26.561 1 59.48 ? C6 TBN 301 A 1 HETATM 11 N N1 TBN . . . B 2 45.736 34.302 25.992 1 59.15 ? N1 TBN 301 A 1 HETATM 12 C C2 TBN . . . B 2 45.868 34.08 24.667 1 58.96 ? C2 TBN 301 A 1 HETATM 13 N N3 TBN . . . B 2 44.784 33.95 23.87 1 58.74 ? N3 TBN 301 A 1 HETATM 14 C C4 TBN . . . B 2 43.522 34.048 24.389 1 58.47 ? C4 TBN 301 A 1 HETATM 15 N N6 TBN . . . B 2 44.349 34.639 27.904 1 59.85 ? N6 TBN 301 A 1 HETATM 16 C C2' TBN . . . B 2 42.804 33.81 21.341 1 54.48 ? C2' TBN 301 A 1 HETATM 17 O O2' TBN . . . B 2 42.249 34.631 20.308 1 54.71 ? O2' TBN 301 A 1 HETATM 18 C C3' TBN . . . B 2 43.043 32.393 20.834 1 53.75 ? C3' TBN 301 A 1 HETATM 19 O O3' TBN . . . B 2 42.729 32.239 19.449 1 52.08 ? O3' TBN 301 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 19 #