data_1Z39 # _model_server_result.job_id Apc1zRnzF7DyUUQ5fBf3Gg _model_server_result.datetime_utc '2024-11-23 03:45:32' _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 1z39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 1Z39 # _exptl.entry_id 1Z39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 252.227 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYINOSINE" _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 1Z39 _cell.length_a 136.8 _cell.length_b 136.8 _cell.length_c 136.8 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z39 _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 2' # _pdbx_struct_assembly.method_details PISA,PQS _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,C _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 4 'crystal symmetry operation' 14_444 -y-1/4,-x-1/4,-z-1/4 0 -1 0 -1 0 0 0 0 -1 -34.2 -34.2 -34.2 5 'crystal symmetry operation' 19_444 -x-1/4,-z-1/4,-y-1/4 -1 0 0 0 0 -1 0 -1 0 -34.2 -34.2 -34.2 6 'crystal symmetry operation' 24_444 -z-1/4,-y-1/4,-x-1/4 0 0 -1 0 -1 0 -1 0 0 -34.2 -34.2 -34.2 # _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 'C10 H12 N4 O4' _chem_comp.formula_weight 252.227 _chem_comp.id 2ND _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYINOSINE" _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 O6 C6 2ND doub 1 n n C6 N1 2ND sing 2 n n C6 C5 2ND sing 3 n n N1 C2 2ND sing 4 n n N1 HN1 2ND sing 5 n n C2 N3 2ND doub 6 n n C2 H2 2ND sing 7 n n N3 C4 2ND sing 8 n n C4 C5 2ND doub 9 n y C4 N9 2ND sing 10 n y C5 N7 2ND sing 11 n y N7 C8 2ND doub 12 n y C8 N9 2ND sing 13 n y C8 H8 2ND sing 14 n n N9 C1' 2ND sing 15 n n C1' O4' 2ND sing 16 n n C1' C2' 2ND sing 17 n n C1' H1' 2ND sing 18 n n O4' C4' 2ND sing 19 n n C2' C3' 2ND sing 20 n n C2' "H2'1" 2ND sing 21 n n C2' "H2'2" 2ND sing 22 n n C3' O3' 2ND sing 23 n n C3' C4' 2ND sing 24 n n C3' H3' 2ND sing 25 n n O3' H1 2ND sing 26 n n C4' C5' 2ND sing 27 n n C4' H4' 2ND sing 28 n n C5' O5' 2ND sing 29 n n C5' "H5'1" 2ND sing 30 n n C5' "H5'2" 2ND sing 31 n n O5' H5' 2ND sing 32 n n # _atom_sites.entry_id 1Z39 _atom_sites.fract_transf_matrix[1][1] 0.00731 _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] 0.00731 _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] 0.00731 _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 2ND A 1 300 300 2ND 2ND . C 3 HOH A 1 301 1 HOH HOH . C 3 HOH A 2 302 2 HOH HOH . C 3 HOH A 3 303 3 HOH HOH . C 3 HOH A 4 304 4 HOH HOH . C 3 HOH A 5 305 5 HOH HOH . C 3 HOH A 6 306 6 HOH HOH . C 3 HOH A 7 307 7 HOH HOH . C 3 HOH A 8 308 8 HOH HOH . C 3 HOH A 9 309 9 HOH HOH . C 3 HOH A 10 310 10 HOH HOH . C 3 HOH A 11 311 11 HOH HOH . C 3 HOH A 12 312 12 HOH HOH . C 3 HOH A 13 313 13 HOH HOH . C 3 HOH A 14 314 14 HOH HOH . C 3 HOH A 15 315 15 HOH HOH . C 3 HOH A 16 316 16 HOH HOH . C 3 HOH A 17 317 17 HOH HOH . C 3 HOH A 18 318 18 HOH HOH . C 3 HOH A 19 319 19 HOH HOH . C 3 HOH A 20 320 20 HOH HOH . C 3 HOH A 21 321 21 HOH HOH . C 3 HOH A 22 322 22 HOH HOH . C 3 HOH A 23 323 23 HOH HOH . C 3 HOH A 24 324 24 HOH HOH . C 3 HOH A 25 325 25 HOH HOH . C 3 HOH A 26 326 26 HOH HOH . C 3 HOH A 27 327 27 HOH HOH . C 3 HOH A 28 328 28 HOH HOH . C 3 HOH A 29 329 29 HOH HOH . C 3 HOH A 30 330 30 HOH HOH . C 3 HOH A 31 331 31 HOH HOH . C 3 HOH A 32 332 32 HOH HOH . C 3 HOH A 33 333 33 HOH HOH . C 3 HOH A 34 334 34 HOH HOH . C 3 HOH A 35 335 35 HOH HOH . C 3 HOH A 36 336 36 HOH HOH . C 3 HOH A 37 337 37 HOH HOH . C 3 HOH A 38 338 38 HOH HOH . C 3 HOH A 39 339 39 HOH HOH . C 3 HOH A 40 340 40 HOH HOH . C 3 HOH A 41 341 41 HOH HOH . C 3 HOH A 42 342 42 HOH HOH . C 3 HOH A 43 343 43 HOH HOH . C 3 HOH A 44 344 44 HOH HOH . C 3 HOH A 45 345 45 HOH HOH . C 3 HOH A 46 346 46 HOH HOH . C 3 HOH A 47 347 47 HOH HOH . C 3 HOH A 48 348 48 HOH HOH . C 3 HOH A 49 349 49 HOH HOH . C 3 HOH A 50 350 50 HOH HOH . C 3 HOH A 51 351 51 HOH HOH . C 3 HOH A 52 352 52 HOH HOH . C 3 HOH A 53 353 53 HOH HOH . C 3 HOH A 54 354 54 HOH HOH . C 3 HOH A 55 355 55 HOH HOH . C 3 HOH A 56 356 56 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 O O6 2ND . . . B 2 -18.325 -43.293 -12.156 1 50.73 ? O6 2ND 300 A 1 HETATM 2 C C6 2ND . . . B 2 -17.962 -42.535 -11.258 1 49.27 ? C6 2ND 300 A 1 HETATM 3 N N1 2ND . . . B 2 -18.278 -41.171 -11.31 1 49.58 ? N1 2ND 300 A 1 HETATM 4 C C2 2ND . . . B 2 -17.84 -40.327 -10.282 1 49.39 ? C2 2ND 300 A 1 HETATM 5 N N3 2ND . . . B 2 -17.138 -40.818 -9.275 1 48.38 ? N3 2ND 300 A 1 HETATM 6 C C4 2ND . . . B 2 -16.822 -42.12 -9.192 1 48.24 ? C4 2ND 300 A 1 HETATM 7 C C5 2ND . . . B 2 -17.224 -43.011 -10.18 1 48.51 ? C5 2ND 300 A 1 HETATM 8 N N7 2ND . . . B 2 -16.786 -44.216 -9.83 1 48.35 ? N7 2ND 300 A 1 HETATM 9 C C8 2ND . . . B 2 -16.14 -44.095 -8.674 1 47.35 ? C8 2ND 300 A 1 HETATM 10 N N9 2ND . . . B 2 -16.158 -42.825 -8.278 1 47.98 ? N9 2ND 300 A 1 HETATM 11 C C1' 2ND . . . B 2 -15.576 -42.327 -7.008 1 46.54 ? C1' 2ND 300 A 1 HETATM 12 O O4' 2ND . . . B 2 -16.297 -42.857 -5.881 1 46.35 ? O4' 2ND 300 A 1 HETATM 13 C C2' 2ND . . . B 2 -15.608 -40.799 -6.884 1 45.54 ? C2' 2ND 300 A 1 HETATM 14 C C3' 2ND . . . B 2 -16.044 -40.603 -5.432 1 43.17 ? C3' 2ND 300 A 1 HETATM 15 O O3' 2ND . . . B 2 -14.924 -40.713 -4.55 1 43.84 ? O3' 2ND 300 A 1 HETATM 16 C C4' 2ND . . . B 2 -17.009 -41.775 -5.256 1 44.02 ? C4' 2ND 300 A 1 HETATM 17 C C5' 2ND . . . B 2 -18.348 -41.562 -5.967 1 41.04 ? C5' 2ND 300 A 1 HETATM 18 O O5' 2ND . . . B 2 -19.093 -42.782 -5.94 1 41.55 ? O5' 2ND 300 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #