data_3RE4 # _model_server_result.job_id y8WgEFC1CtqmSss-vjsLRw _model_server_result.datetime_utc '2024-11-13 06:53:35' _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 3re4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":259}' # _entry.id 3RE4 # _exptl.entry_id 3RE4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.263 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile _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 90.17 _cell.angle_gamma 90 _cell.entry_id 3RE4 _cell.length_a 52.814 _cell.length_b 72.607 _cell.length_c 60.561 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RE4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C12 H13 N5 O4' _chem_comp.formula_weight 291.263 _chem_comp.id TO1 _chem_comp.mon_nstd_flag . _chem_comp.name 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile _chem_comp.type non-polymer _chem_comp.pdbx_synonyms TOYOCAMYCIN # 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 C N TO1 sing 293 n n C O TO1 sing 294 n n C C9 TO1 sing 295 n n N C2 TO1 sing 296 n y N C7 TO1 sing 297 n y O C11 TO1 sing 298 n n C2 N2 TO1 doub 299 n y C2 C5 TO1 sing 300 n y N2 C3 TO1 sing 301 n y O2 C9 TO1 sing 302 n n C3 N3 TO1 doub 303 n y N3 C4 TO1 sing 304 n y O3 C10 TO1 sing 305 n n C4 C5 TO1 doub 306 n y C4 N5 TO1 sing 307 n n N4 C8 TO1 trip 308 n n O4 C12 TO1 sing 309 n n C5 C6 TO1 sing 310 n y C6 C7 TO1 doub 311 n y C6 C8 TO1 sing 312 n n C9 C10 TO1 sing 313 n n C10 C11 TO1 sing 314 n n C11 C12 TO1 sing 315 n n C H TO1 sing 316 n n O2 HO2 TO1 sing 317 n n C3 H3 TO1 sing 318 n n O3 HO3 TO1 sing 319 n n O4 HO4 TO1 sing 320 n n N5 HN5 TO1 sing 321 n n N5 HN5A TO1 sing 322 n n C7 H7 TO1 sing 323 n n C9 H9 TO1 sing 324 n n C10 H10 TO1 sing 325 n n C11 H11 TO1 sing 326 n n C12 H12 TO1 sing 327 n n C12 H12A TO1 sing 328 n n # _atom_sites.entry_id 3RE4 _atom_sites.fract_transf_matrix[1][1] 0.018934 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000056 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013773 _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] 0.016512 _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 TO1 A 1 259 259 TO1 TO1 . D 2 TO1 B 1 259 259 TO1 TO1 . E 3 HOH A 1 260 2 HOH HOH . E 3 HOH A 2 261 5 HOH HOH . E 3 HOH A 3 262 6 HOH HOH . E 3 HOH A 4 263 7 HOH HOH . E 3 HOH A 5 264 9 HOH HOH . E 3 HOH A 6 265 10 HOH HOH . E 3 HOH A 7 266 11 HOH HOH . E 3 HOH A 8 267 13 HOH HOH . E 3 HOH A 9 268 15 HOH HOH . E 3 HOH A 10 269 17 HOH HOH . E 3 HOH A 11 270 19 HOH HOH . E 3 HOH A 12 271 21 HOH HOH . E 3 HOH A 13 272 23 HOH HOH . E 3 HOH A 14 273 24 HOH HOH . E 3 HOH A 15 274 25 HOH HOH . E 3 HOH A 16 275 29 HOH HOH . E 3 HOH A 17 276 30 HOH HOH . E 3 HOH A 18 277 31 HOH HOH . E 3 HOH A 19 278 33 HOH HOH . E 3 HOH A 20 279 34 HOH HOH . E 3 HOH A 21 280 35 HOH HOH . E 3 HOH A 22 281 38 HOH HOH . E 3 HOH A 23 282 39 HOH HOH . E 3 HOH A 24 283 43 HOH HOH . E 3 HOH A 25 284 45 HOH HOH . E 3 HOH A 26 285 46 HOH HOH . E 3 HOH A 27 286 50 HOH HOH . E 3 HOH A 28 287 51 HOH HOH . E 3 HOH A 29 288 53 HOH HOH . E 3 HOH A 30 289 54 HOH HOH . E 3 HOH A 31 290 55 HOH HOH . E 3 HOH A 32 291 59 HOH HOH . E 3 HOH A 33 292 62 HOH HOH . E 3 HOH A 34 293 64 HOH HOH . E 3 HOH A 35 294 65 HOH HOH . E 3 HOH A 36 295 66 HOH HOH . E 3 HOH A 37 296 67 HOH HOH . E 3 HOH A 38 297 69 HOH HOH . E 3 HOH A 39 298 70 HOH HOH . E 3 HOH A 40 299 78 HOH HOH . E 3 HOH A 41 300 82 HOH HOH . E 3 HOH A 42 301 85 HOH HOH . E 3 HOH A 43 302 87 HOH HOH . E 3 HOH A 44 303 89 HOH HOH . E 3 HOH A 45 304 93 HOH HOH . E 3 HOH A 46 305 94 HOH HOH . E 3 HOH A 47 306 99 HOH HOH . E 3 HOH A 48 307 100 HOH HOH . E 3 HOH A 49 308 102 HOH HOH . E 3 HOH A 50 309 104 HOH HOH . E 3 HOH A 51 310 105 HOH HOH . E 3 HOH A 52 311 106 HOH HOH . E 3 HOH A 53 312 108 HOH HOH . E 3 HOH A 54 313 111 HOH HOH . E 3 HOH A 55 314 116 HOH HOH . E 3 HOH A 56 315 117 HOH HOH . E 3 HOH A 57 316 118 HOH HOH . E 3 HOH A 58 317 120 HOH HOH . E 3 HOH A 59 318 121 HOH HOH . E 3 HOH A 60 319 123 HOH HOH . E 3 HOH A 61 320 124 HOH HOH . E 3 HOH A 62 321 127 HOH HOH . E 3 HOH A 63 322 129 HOH HOH . E 3 HOH A 64 323 133 HOH HOH . E 3 HOH A 65 324 137 HOH HOH . E 3 HOH A 66 325 140 HOH HOH . E 3 HOH A 67 326 144 HOH HOH . E 3 HOH A 68 327 145 HOH HOH . E 3 HOH A 69 328 146 HOH HOH . E 3 HOH A 70 329 148 HOH HOH . E 3 HOH A 71 330 149 HOH HOH . E 3 HOH A 72 331 151 HOH HOH . E 3 HOH A 73 332 152 HOH HOH . E 3 HOH A 74 333 158 HOH HOH . E 3 HOH A 75 334 160 HOH HOH . E 3 HOH A 76 335 162 HOH HOH . E 3 HOH A 77 336 163 HOH HOH . E 3 HOH A 78 337 164 HOH HOH . E 3 HOH A 79 338 165 HOH HOH . E 3 HOH A 80 339 168 HOH HOH . E 3 HOH A 81 340 169 HOH HOH . E 3 HOH A 82 341 170 HOH HOH . E 3 HOH A 83 342 174 HOH HOH . E 3 HOH A 84 343 175 HOH HOH . F 3 HOH B 1 260 1 HOH HOH . F 3 HOH B 2 261 3 HOH HOH . F 3 HOH B 3 262 4 HOH HOH . F 3 HOH B 4 263 8 HOH HOH . F 3 HOH B 5 264 12 HOH HOH . F 3 HOH B 6 265 14 HOH HOH . F 3 HOH B 7 266 16 HOH HOH . F 3 HOH B 8 267 18 HOH HOH . F 3 HOH B 9 268 20 HOH HOH . F 3 HOH B 10 269 22 HOH HOH . F 3 HOH B 11 270 26 HOH HOH . F 3 HOH B 12 271 27 HOH HOH . F 3 HOH B 13 272 28 HOH HOH . F 3 HOH B 14 273 32 HOH HOH . F 3 HOH B 15 274 36 HOH HOH . F 3 HOH B 16 275 37 HOH HOH . F 3 HOH B 17 276 40 HOH HOH . F 3 HOH B 18 277 41 HOH HOH . F 3 HOH B 19 278 42 HOH HOH . F 3 HOH B 20 279 44 HOH HOH . F 3 HOH B 21 280 47 HOH HOH . F 3 HOH B 22 281 48 HOH HOH . F 3 HOH B 23 282 49 HOH HOH . F 3 HOH B 24 283 52 HOH HOH . F 3 HOH B 25 284 56 HOH HOH . F 3 HOH B 26 285 57 HOH HOH . F 3 HOH B 27 286 58 HOH HOH . F 3 HOH B 28 287 60 HOH HOH . F 3 HOH B 29 288 61 HOH HOH . F 3 HOH B 30 289 63 HOH HOH . F 3 HOH B 31 290 68 HOH HOH . F 3 HOH B 32 291 71 HOH HOH . F 3 HOH B 33 292 72 HOH HOH . F 3 HOH B 34 293 74 HOH HOH . F 3 HOH B 35 294 75 HOH HOH . F 3 HOH B 36 295 76 HOH HOH . F 3 HOH B 37 296 77 HOH HOH . F 3 HOH B 38 297 79 HOH HOH . F 3 HOH B 39 298 80 HOH HOH . F 3 HOH B 40 299 81 HOH HOH . F 3 HOH B 41 300 83 HOH HOH . F 3 HOH B 42 301 84 HOH HOH . F 3 HOH B 43 302 86 HOH HOH . F 3 HOH B 44 303 88 HOH HOH . F 3 HOH B 45 304 90 HOH HOH . F 3 HOH B 46 305 91 HOH HOH . F 3 HOH B 47 306 92 HOH HOH . F 3 HOH B 48 307 95 HOH HOH . F 3 HOH B 49 308 96 HOH HOH . F 3 HOH B 50 309 97 HOH HOH . F 3 HOH B 51 310 98 HOH HOH . F 3 HOH B 52 311 101 HOH HOH . F 3 HOH B 53 312 107 HOH HOH . F 3 HOH B 54 313 109 HOH HOH . F 3 HOH B 55 314 110 HOH HOH . F 3 HOH B 56 315 112 HOH HOH . F 3 HOH B 57 316 113 HOH HOH . F 3 HOH B 58 317 114 HOH HOH . F 3 HOH B 59 318 115 HOH HOH . F 3 HOH B 60 319 119 HOH HOH . F 3 HOH B 61 320 122 HOH HOH . F 3 HOH B 62 321 125 HOH HOH . F 3 HOH B 63 322 126 HOH HOH . F 3 HOH B 64 323 128 HOH HOH . F 3 HOH B 65 324 130 HOH HOH . F 3 HOH B 66 325 131 HOH HOH . F 3 HOH B 67 326 132 HOH HOH . F 3 HOH B 68 327 134 HOH HOH . F 3 HOH B 69 328 135 HOH HOH . F 3 HOH B 70 329 136 HOH HOH . F 3 HOH B 71 330 138 HOH HOH . F 3 HOH B 72 331 139 HOH HOH . F 3 HOH B 73 332 141 HOH HOH . F 3 HOH B 74 333 142 HOH HOH . F 3 HOH B 75 334 147 HOH HOH . F 3 HOH B 76 335 150 HOH HOH . F 3 HOH B 77 336 153 HOH HOH . F 3 HOH B 78 337 154 HOH HOH . F 3 HOH B 79 338 155 HOH HOH . F 3 HOH B 80 339 156 HOH HOH . F 3 HOH B 81 340 157 HOH HOH . F 3 HOH B 82 341 159 HOH HOH . F 3 HOH B 83 342 161 HOH HOH . F 3 HOH B 84 343 166 HOH HOH . F 3 HOH B 85 344 167 HOH HOH . F 3 HOH B 86 345 171 HOH HOH . F 3 HOH B 87 346 172 HOH HOH . F 3 HOH B 88 347 173 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 C TO1 . . . C 2 7.615 2.143 25.336 1 24.31 ? C TO1 259 A 1 HETATM 2 N N TO1 . . . C 2 8.473 2.249 26.526 1 23.08 ? N TO1 259 A 1 HETATM 3 O O TO1 . . . C 2 7.323 0.789 24.983 1 27.56 ? O TO1 259 A 1 HETATM 4 C C2 TO1 . . . C 2 8.455 3.3 27.352 1 27.66 ? C2 TO1 259 A 1 HETATM 5 N N2 TO1 . . . C 2 7.757 4.438 27.336 1 27.59 ? N2 TO1 259 A 1 HETATM 6 O O2 TO1 . . . C 2 7.16 3.305 23.226 1 32.37 ? O2 TO1 259 A 1 HETATM 7 C C3 TO1 . . . C 2 7.887 5.38 28.249 1 20.87 ? C3 TO1 259 A 1 HETATM 8 N N3 TO1 . . . C 2 8.766 5.21 29.239 1 25.54 ? N3 TO1 259 A 1 HETATM 9 O O3 TO1 . . . C 2 8.471 1.929 21.951 1 40.87 ? O3 TO1 259 A 1 HETATM 10 C C4 TO1 . . . C 2 9.543 4.136 29.431 1 21.85 ? C4 TO1 259 A 1 HETATM 11 N N4 TO1 . . . C 2 11.803 0.645 29.376 1 26.27 ? N4 TO1 259 A 1 HETATM 12 O O4 TO1 . . . C 2 10.111 -0.494 24.119 1 35.67 ? O4 TO1 259 A 1 HETATM 13 C C5 TO1 . . . C 2 9.417 3.068 28.444 1 23.78 ? C5 TO1 259 A 1 HETATM 14 N N5 TO1 . . . C 2 10.424 3.978 30.445 1 15.47 ? N5 TO1 259 A 1 HETATM 15 C C6 TO1 . . . C 2 9.98 1.75 28.093 1 25.23 ? C6 TO1 259 A 1 HETATM 16 C C7 TO1 . . . C 2 9.346 1.26 26.891 1 21.67 ? C7 TO1 259 A 1 HETATM 17 C C8 TO1 . . . C 2 10.889 1.086 28.81 1 25.49 ? C8 TO1 259 A 1 HETATM 18 C C9 TO1 . . . C 2 8.197 2.786 24.092 1 34.65 ? C9 TO1 259 A 1 HETATM 19 C C10 TO1 . . . C 2 8.76 1.643 23.313 1 31.65 ? C10 TO1 259 A 1 HETATM 20 C C11 TO1 . . . C 2 7.918 0.449 23.719 1 29.19 ? C11 TO1 259 A 1 HETATM 21 C C12 TO1 . . . C 2 8.732 -0.822 23.884 1 33.18 ? C12 TO1 259 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #