data_2ZI3 # _model_server_result.job_id wn3E6-ODZFaw9KXRnU9Z1w _model_server_result.datetime_utc '2024-11-04 22:18:44' _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 2zi3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 2ZI3 # _exptl.entry_id 2ZI3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _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 2ZI3 _cell.length_a 52.44 _cell.length_b 133.29 _cell.length_c 156.73 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZI3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,E,F,G,H _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 ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 3D1 _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-DEOXYADENOSINE" # 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' 3D1 sing 1 n n O5' H5' 3D1 sing 2 n n C5' C4' 3D1 sing 3 n n C5' "H5'1" 3D1 sing 4 n n C5' "H5'2" 3D1 sing 5 n n C4' O4' 3D1 sing 6 n n C4' C3' 3D1 sing 7 n n C4' H4' 3D1 sing 8 n n O4' C1' 3D1 sing 9 n n C1' N9 3D1 sing 10 n n C1' C2' 3D1 sing 11 n n C1' H1' 3D1 sing 12 n n N9 C4 3D1 sing 13 n y N9 C8 3D1 sing 14 n y C4 N3 3D1 doub 15 n y C4 C5 3D1 sing 16 n y N3 C2 3D1 sing 17 n y C2 N1 3D1 doub 18 n y C2 H2 3D1 sing 19 n n N1 C6 3D1 sing 20 n y C6 N6 3D1 sing 21 n n C6 C5 3D1 doub 22 n y N6 HN61 3D1 sing 23 n n N6 HN62 3D1 sing 24 n n C5 N7 3D1 sing 25 n y N7 C8 3D1 doub 26 n y C8 H8 3D1 sing 27 n n C2' C3' 3D1 sing 28 n n C2' "H2'1" 3D1 sing 29 n n C2' "H2'2" 3D1 sing 30 n n C3' O3' 3D1 sing 31 n n C3' H3' 3D1 sing 32 n n O3' H1 3D1 sing 33 n n # _atom_sites.entry_id 2ZI3 _atom_sites.fract_transf_matrix[1][1] 0.019069 _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] 0.007502 _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] 0.00638 _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 ADP A 1 301 301 ADP ADP . D 3 3D1 A 1 302 302 3D1 DAD . E 2 ADP B 1 301 301 ADP ADP . F 3 3D1 B 1 302 302 3D1 DAD . G 4 HOH A 1 303 2 HOH HOH . G 4 HOH A 2 304 3 HOH HOH . G 4 HOH A 3 305 4 HOH HOH . G 4 HOH A 4 306 7 HOH HOH . G 4 HOH A 5 307 8 HOH HOH . G 4 HOH A 6 308 14 HOH HOH . G 4 HOH A 7 309 17 HOH HOH . G 4 HOH A 8 310 19 HOH HOH . G 4 HOH A 9 311 20 HOH HOH . G 4 HOH A 10 312 21 HOH HOH . G 4 HOH A 11 313 22 HOH HOH . G 4 HOH A 12 314 26 HOH HOH . G 4 HOH A 13 315 30 HOH HOH . G 4 HOH A 14 316 32 HOH HOH . G 4 HOH A 15 317 34 HOH HOH . G 4 HOH A 16 318 35 HOH HOH . G 4 HOH A 17 319 40 HOH HOH . G 4 HOH A 18 320 41 HOH HOH . G 4 HOH A 19 321 42 HOH HOH . G 4 HOH A 20 322 43 HOH HOH . G 4 HOH A 21 323 44 HOH HOH . G 4 HOH A 22 324 70 HOH HOH . G 4 HOH A 23 325 73 HOH HOH . G 4 HOH A 24 326 75 HOH HOH . G 4 HOH A 25 327 77 HOH HOH . G 4 HOH A 26 328 86 HOH HOH . G 4 HOH A 27 329 87 HOH HOH . G 4 HOH A 28 330 88 HOH HOH . G 4 HOH A 29 331 90 HOH HOH . G 4 HOH A 30 332 93 HOH HOH . G 4 HOH A 31 333 96 HOH HOH . G 4 HOH A 32 334 97 HOH HOH . G 4 HOH A 33 335 98 HOH HOH . G 4 HOH A 34 336 100 HOH HOH . G 4 HOH A 35 337 102 HOH HOH . G 4 HOH A 36 338 104 HOH HOH . G 4 HOH A 37 339 105 HOH HOH . G 4 HOH A 38 340 106 HOH HOH . G 4 HOH A 39 341 109 HOH HOH . G 4 HOH A 40 342 110 HOH HOH . G 4 HOH A 41 343 111 HOH HOH . G 4 HOH A 42 344 113 HOH HOH . G 4 HOH A 43 345 114 HOH HOH . G 4 HOH A 44 346 117 HOH HOH . G 4 HOH A 45 347 120 HOH HOH . G 4 HOH A 46 348 122 HOH HOH . G 4 HOH A 47 349 123 HOH HOH . G 4 HOH A 48 350 125 HOH HOH . G 4 HOH A 49 351 127 HOH HOH . G 4 HOH A 50 352 128 HOH HOH . G 4 HOH A 51 353 129 HOH HOH . G 4 HOH A 52 354 130 HOH HOH . G 4 HOH A 53 355 131 HOH HOH . G 4 HOH A 54 356 136 HOH HOH . G 4 HOH A 55 357 137 HOH HOH . G 4 HOH A 56 358 141 HOH HOH . G 4 HOH A 57 359 143 HOH HOH . G 4 HOH A 58 360 144 HOH HOH . G 4 HOH A 59 361 115 HOH HOH . G 4 HOH A 60 362 138 HOH HOH . H 4 HOH B 1 303 1 HOH HOH . H 4 HOH B 2 304 5 HOH HOH . H 4 HOH B 3 305 6 HOH HOH . H 4 HOH B 4 306 9 HOH HOH . H 4 HOH B 5 307 10 HOH HOH . H 4 HOH B 6 308 11 HOH HOH . H 4 HOH B 7 309 12 HOH HOH . H 4 HOH B 8 310 13 HOH HOH . H 4 HOH B 9 311 15 HOH HOH . H 4 HOH B 10 312 16 HOH HOH . H 4 HOH B 11 313 18 HOH HOH . H 4 HOH B 12 314 24 HOH HOH . H 4 HOH B 13 315 27 HOH HOH . H 4 HOH B 14 316 28 HOH HOH . H 4 HOH B 15 317 29 HOH HOH . H 4 HOH B 16 318 31 HOH HOH . H 4 HOH B 17 319 36 HOH HOH . H 4 HOH B 18 320 37 HOH HOH . H 4 HOH B 19 321 39 HOH HOH . H 4 HOH B 20 322 45 HOH HOH . H 4 HOH B 21 323 71 HOH HOH . H 4 HOH B 22 324 74 HOH HOH . H 4 HOH B 23 325 78 HOH HOH . H 4 HOH B 24 326 79 HOH HOH . H 4 HOH B 25 327 80 HOH HOH . H 4 HOH B 26 328 81 HOH HOH . H 4 HOH B 27 329 82 HOH HOH . H 4 HOH B 28 330 89 HOH HOH . H 4 HOH B 29 331 91 HOH HOH . H 4 HOH B 30 332 92 HOH HOH . H 4 HOH B 31 333 94 HOH HOH . H 4 HOH B 32 334 95 HOH HOH . H 4 HOH B 33 335 101 HOH HOH . H 4 HOH B 34 336 107 HOH HOH . H 4 HOH B 35 337 108 HOH HOH . H 4 HOH B 36 339 119 HOH HOH . H 4 HOH B 37 340 132 HOH HOH . H 4 HOH B 38 341 133 HOH HOH . H 4 HOH B 39 342 134 HOH HOH . H 4 HOH B 40 343 135 HOH HOH . H 4 HOH B 41 345 139 HOH HOH . H 4 HOH B 42 346 140 HOH HOH . H 4 HOH B 43 347 142 HOH HOH . H 4 HOH B 44 350 124 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 O5' 3D1 . . . F 3 33.549 96.06 96.123 1 41.71 ? O5' 3D1 302 B 1 HETATM 2 C C5' 3D1 . . . F 3 34.286 97.138 96.716 1 39.95 ? C5' 3D1 302 B 1 HETATM 3 C C4' 3D1 . . . F 3 35.775 96.833 96.586 1 37.46 ? C4' 3D1 302 B 1 HETATM 4 O O4' 3D1 . . . F 3 36.02 95.425 96.412 1 35.15 ? O4' 3D1 302 B 1 HETATM 5 C C1' 3D1 . . . F 3 36.546 95.171 95.109 1 32.56 ? C1' 3D1 302 B 1 HETATM 6 N N9 3D1 . . . F 3 36.003 93.928 94.53 1 31.29 ? N9 3D1 302 B 1 HETATM 7 C C4 3D1 . . . F 3 36.705 93.007 93.886 1 29.81 ? C4 3D1 302 B 1 HETATM 8 N N3 3D1 . . . F 3 38.022 92.928 93.579 1 29.76 ? N3 3D1 302 B 1 HETATM 9 C C2 3D1 . . . F 3 38.581 91.795 92.851 1 30.88 ? C2 3D1 302 B 1 HETATM 10 N N1 3D1 . . . F 3 37.594 90.766 92.498 1 32.39 ? N1 3D1 302 B 1 HETATM 11 C C6 3D1 . . . F 3 36.279 90.858 92.796 1 30.61 ? C6 3D1 302 B 1 HETATM 12 N N6 3D1 . . . F 3 35.364 89.907 92.483 1 31.23 ? N6 3D1 302 B 1 HETATM 13 C C5 3D1 . . . F 3 35.817 92.025 93.517 1 27.99 ? C5 3D1 302 B 1 HETATM 14 N N7 3D1 . . . F 3 34.604 92.332 93.935 1 29.58 ? N7 3D1 302 B 1 HETATM 15 C C8 3D1 . . . F 3 34.725 93.524 94.563 1 32.04 ? C8 3D1 302 B 1 HETATM 16 C C2' 3D1 . . . F 3 36.193 96.416 94.291 1 35.63 ? C2' 3D1 302 B 1 HETATM 17 C C3' 3D1 . . . F 3 36.293 97.498 95.347 1 35.29 ? C3' 3D1 302 B 1 HETATM 18 O O3' 3D1 . . . F 3 37.674 97.73 95.602 1 33.85 ? O3' 3D1 302 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #