data_2DFN # _model_server_result.job_id BEomi09PEoLuLHSZJqIazg _model_server_result.datetime_utc '2024-10-20 19:38:10' _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 2dfn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":177}' # _entry.id 2DFN # _exptl.entry_id 2DFN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 2DFN _cell.length_a 63.296 _cell.length_b 63.296 _cell.length_c 91.61 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DFN _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 2DFN _atom_sites.fract_transf_matrix[1][1] 0.015799 _atom_sites.fract_transf_matrix[1][2] 0.009121 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018243 _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] 0.010916 _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 CL A 1 1180 180 CL CL . C 3 ADP A 1 177 177 ADP ADP . D 4 SKM A 1 500 500 SKM SHI . E 5 HOH A 1 178 178 HOH HOH . E 5 HOH A 2 179 179 HOH HOH . E 5 HOH A 3 180 180 HOH HOH . E 5 HOH A 4 181 181 HOH HOH . E 5 HOH A 5 182 182 HOH HOH . E 5 HOH A 6 183 183 HOH HOH . E 5 HOH A 7 184 184 HOH HOH . E 5 HOH A 8 185 185 HOH HOH . E 5 HOH A 9 186 186 HOH HOH . E 5 HOH A 10 187 187 HOH HOH . E 5 HOH A 11 188 188 HOH HOH . E 5 HOH A 12 189 189 HOH HOH . E 5 HOH A 13 190 190 HOH HOH . E 5 HOH A 14 191 191 HOH HOH . E 5 HOH A 15 192 192 HOH HOH . E 5 HOH A 16 193 193 HOH HOH . E 5 HOH A 17 194 194 HOH HOH . E 5 HOH A 18 195 195 HOH HOH . E 5 HOH A 19 196 196 HOH HOH . E 5 HOH A 20 197 197 HOH HOH . E 5 HOH A 21 198 198 HOH HOH . E 5 HOH A 22 199 199 HOH HOH . E 5 HOH A 23 200 200 HOH HOH . E 5 HOH A 24 201 201 HOH HOH . E 5 HOH A 25 202 202 HOH HOH . E 5 HOH A 26 203 203 HOH HOH . E 5 HOH A 27 204 204 HOH HOH . E 5 HOH A 28 205 205 HOH HOH . E 5 HOH A 29 206 206 HOH HOH . E 5 HOH A 30 208 208 HOH HOH . E 5 HOH A 31 209 209 HOH HOH . E 5 HOH A 32 210 210 HOH HOH . E 5 HOH A 33 211 211 HOH HOH . E 5 HOH A 34 212 212 HOH HOH . E 5 HOH A 35 213 213 HOH HOH . E 5 HOH A 36 214 214 HOH HOH . E 5 HOH A 37 215 215 HOH HOH . E 5 HOH A 38 216 216 HOH HOH . E 5 HOH A 39 218 218 HOH HOH . E 5 HOH A 40 219 219 HOH HOH . E 5 HOH A 41 220 220 HOH HOH . E 5 HOH A 42 221 221 HOH HOH . E 5 HOH A 43 222 222 HOH HOH . E 5 HOH A 44 223 223 HOH HOH . E 5 HOH A 45 224 224 HOH HOH . E 5 HOH A 46 225 225 HOH HOH . E 5 HOH A 47 226 226 HOH HOH . E 5 HOH A 48 227 227 HOH HOH . E 5 HOH A 49 228 228 HOH HOH . E 5 HOH A 50 229 229 HOH HOH . E 5 HOH A 51 230 230 HOH HOH . E 5 HOH A 52 231 231 HOH HOH . E 5 HOH A 53 232 232 HOH HOH . E 5 HOH A 54 233 233 HOH HOH . E 5 HOH A 55 234 234 HOH HOH . E 5 HOH A 56 235 235 HOH HOH . E 5 HOH A 57 237 237 HOH HOH . E 5 HOH A 58 238 238 HOH HOH . E 5 HOH A 59 239 239 HOH HOH . E 5 HOH A 60 240 240 HOH HOH . E 5 HOH A 61 241 241 HOH HOH . E 5 HOH A 62 242 242 HOH HOH . E 5 HOH A 63 243 243 HOH HOH . E 5 HOH A 64 244 244 HOH HOH . E 5 HOH A 65 245 245 HOH HOH . E 5 HOH A 66 246 246 HOH HOH . E 5 HOH A 67 247 247 HOH HOH . E 5 HOH A 68 248 248 HOH HOH . E 5 HOH A 69 249 249 HOH HOH . E 5 HOH A 70 250 250 HOH HOH . E 5 HOH A 71 251 251 HOH HOH . E 5 HOH A 72 252 252 HOH HOH . E 5 HOH A 73 253 253 HOH HOH . E 5 HOH A 74 254 254 HOH HOH . E 5 HOH A 75 255 255 HOH HOH . E 5 HOH A 76 256 256 HOH HOH . E 5 HOH A 77 257 257 HOH HOH . E 5 HOH A 78 258 258 HOH HOH . E 5 HOH A 79 259 259 HOH HOH . E 5 HOH A 80 260 260 HOH HOH . E 5 HOH A 81 261 261 HOH HOH . E 5 HOH A 82 262 262 HOH HOH . E 5 HOH A 83 263 263 HOH HOH . E 5 HOH A 84 264 264 HOH HOH . E 5 HOH A 85 265 265 HOH HOH . E 5 HOH A 86 266 266 HOH HOH . E 5 HOH A 87 267 267 HOH HOH . E 5 HOH A 88 268 268 HOH HOH . E 5 HOH A 89 269 269 HOH HOH . E 5 HOH A 90 271 271 HOH HOH . E 5 HOH A 91 272 272 HOH HOH . E 5 HOH A 92 273 273 HOH HOH . E 5 HOH A 93 274 274 HOH HOH . E 5 HOH A 94 275 275 HOH HOH . E 5 HOH A 95 276 276 HOH HOH . E 5 HOH A 96 277 277 HOH HOH . E 5 HOH A 97 278 278 HOH HOH . E 5 HOH A 98 279 279 HOH HOH . E 5 HOH A 99 280 280 HOH HOH . E 5 HOH A 100 281 281 HOH HOH . E 5 HOH A 101 282 282 HOH HOH . E 5 HOH A 102 283 283 HOH HOH . E 5 HOH A 103 284 284 HOH HOH . E 5 HOH A 104 285 285 HOH HOH . E 5 HOH A 105 286 286 HOH HOH . E 5 HOH A 106 287 287 HOH HOH . E 5 HOH A 107 288 288 HOH HOH . E 5 HOH A 108 289 289 HOH HOH . E 5 HOH A 109 290 290 HOH HOH . E 5 HOH A 110 291 291 HOH HOH . E 5 HOH A 111 292 292 HOH HOH . E 5 HOH A 112 293 293 HOH HOH . E 5 HOH A 113 294 294 HOH HOH . E 5 HOH A 114 295 295 HOH HOH . E 5 HOH A 115 296 296 HOH HOH . E 5 HOH A 116 297 297 HOH HOH . E 5 HOH A 117 300 300 HOH HOH . E 5 HOH A 118 301 301 HOH HOH . E 5 HOH A 119 302 302 HOH HOH . E 5 HOH A 120 303 303 HOH HOH . E 5 HOH A 121 304 304 HOH HOH . E 5 HOH A 122 305 305 HOH HOH . E 5 HOH A 123 306 306 HOH HOH . E 5 HOH A 124 307 307 HOH HOH . E 5 HOH A 125 308 308 HOH HOH . E 5 HOH A 126 309 309 HOH HOH . E 5 HOH A 127 310 310 HOH HOH . E 5 HOH A 128 311 311 HOH HOH . E 5 HOH A 129 312 312 HOH HOH . E 5 HOH A 130 313 313 HOH HOH . E 5 HOH A 131 314 314 HOH HOH . E 5 HOH A 132 315 315 HOH HOH . E 5 HOH A 133 316 316 HOH HOH . E 5 HOH A 134 317 317 HOH HOH . E 5 HOH A 135 318 318 HOH HOH . E 5 HOH A 136 319 319 HOH HOH . E 5 HOH A 137 320 320 HOH HOH . E 5 HOH A 138 321 321 HOH HOH . E 5 HOH A 139 322 322 HOH HOH . E 5 HOH A 140 323 323 HOH HOH . E 5 HOH A 141 324 324 HOH HOH . E 5 HOH A 142 325 325 HOH HOH . E 5 HOH A 143 326 326 HOH HOH . E 5 HOH A 144 327 327 HOH HOH . E 5 HOH A 145 328 328 HOH HOH . E 5 HOH A 146 329 329 HOH HOH . E 5 HOH A 147 330 330 HOH HOH . E 5 HOH A 148 331 331 HOH HOH . E 5 HOH A 149 332 332 HOH HOH . E 5 HOH A 150 333 333 HOH HOH . E 5 HOH A 151 334 334 HOH HOH . E 5 HOH A 152 335 335 HOH HOH . E 5 HOH A 153 336 336 HOH HOH . E 5 HOH A 154 337 337 HOH HOH . E 5 HOH A 155 338 338 HOH HOH . E 5 HOH A 156 339 339 HOH HOH . E 5 HOH A 157 340 340 HOH HOH . E 5 HOH A 158 341 341 HOH HOH . E 5 HOH A 159 342 342 HOH HOH . E 5 HOH A 160 343 343 HOH HOH . E 5 HOH A 161 344 344 HOH HOH . E 5 HOH A 162 345 345 HOH HOH . E 5 HOH A 163 346 346 HOH HOH . E 5 HOH A 164 347 347 HOH HOH . E 5 HOH A 165 348 348 HOH HOH . E 5 HOH A 166 349 349 HOH HOH . E 5 HOH A 167 350 350 HOH HOH . E 5 HOH A 168 351 351 HOH HOH . E 5 HOH A 169 352 352 HOH HOH . E 5 HOH A 170 353 353 HOH HOH . E 5 HOH A 171 354 354 HOH HOH . E 5 HOH A 172 355 355 HOH HOH . E 5 HOH A 173 356 356 HOH HOH . E 5 HOH A 174 357 357 HOH HOH . E 5 HOH A 175 358 358 HOH HOH . E 5 HOH A 176 359 359 HOH HOH . E 5 HOH A 177 360 360 HOH HOH . E 5 HOH A 178 361 361 HOH HOH . E 5 HOH A 179 362 362 HOH HOH . E 5 HOH A 180 363 363 HOH HOH . E 5 HOH A 181 364 364 HOH HOH . E 5 HOH A 182 365 365 HOH HOH . E 5 HOH A 183 366 366 HOH HOH . E 5 HOH A 184 367 367 HOH HOH . E 5 HOH A 185 368 368 HOH HOH . E 5 HOH A 186 369 369 HOH HOH . E 5 HOH A 187 370 370 HOH HOH . E 5 HOH A 188 371 371 HOH HOH . E 5 HOH A 189 372 372 HOH HOH . E 5 HOH A 190 373 373 HOH HOH . E 5 HOH A 191 398 398 HOH HOH . E 5 HOH A 192 399 399 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 P PB ADP . . . C 3 -21.22 -8.772 16.958 1 19.22 ? PB ADP 177 A 1 HETATM 2 O O1B ADP . . . C 3 -22.302 -9.779 17.109 1 14.89 ? O1B ADP 177 A 1 HETATM 3 O O2B ADP . . . C 3 -20.575 -8.565 18.299 1 21.22 ? O2B ADP 177 A 1 HETATM 4 O O3B ADP . . . C 3 -20.288 -8.944 15.78 1 23.86 ? O3B ADP 177 A 1 HETATM 5 P PA ADP . . . C 3 -21.71 -5.888 17.039 1 22.16 ? PA ADP 177 A 1 HETATM 6 O O1A ADP . . . C 3 -20.284 -5.581 16.711 1 20.75 ? O1A ADP 177 A 1 HETATM 7 O O2A ADP . . . C 3 -22.235 -5.623 18.413 1 21.63 ? O2A ADP 177 A 1 HETATM 8 O O3A ADP . . . C 3 -22.049 -7.407 16.595 1 20.45 ? O3A ADP 177 A 1 HETATM 9 O O5' ADP . . . C 3 -22.724 -5.055 16.092 1 24.52 ? O5' ADP 177 A 1 HETATM 10 C C5' ADP . . . C 3 -22.395 -4.82 14.709 1 26.07 ? C5' ADP 177 A 1 HETATM 11 C C4' ADP . . . C 3 -22.89 -3.442 14.299 1 22.41 ? C4' ADP 177 A 1 HETATM 12 O O4' ADP . . . C 3 -24.296 -3.532 14.191 1 22.57 ? O4' ADP 177 A 1 HETATM 13 C C3' ADP . . . C 3 -22.553 -2.343 15.316 1 24.93 ? C3' ADP 177 A 1 HETATM 14 O O3' ADP . . . C 3 -22.298 -1.08 14.687 1 25.2 ? O3' ADP 177 A 1 HETATM 15 C C2' ADP . . . C 3 -23.834 -2.11 16.084 1 20.73 ? C2' ADP 177 A 1 HETATM 16 O O2' ADP . . . C 3 -23.866 -0.697 16.257 1 27.61 ? O2' ADP 177 A 1 HETATM 17 C C1' ADP . . . C 3 -24.896 -2.601 15.087 1 13.72 ? C1' ADP 177 A 1 HETATM 18 N N9 ADP . . . C 3 -26.042 -3.187 15.788 1 23.42 ? N9 ADP 177 A 1 HETATM 19 C C8 ADP . . . C 3 -25.982 -4.143 16.738 1 18.68 ? C8 ADP 177 A 1 HETATM 20 N N7 ADP . . . C 3 -27.218 -4.458 17.133 1 24.17 ? N7 ADP 177 A 1 HETATM 21 C C5 ADP . . . C 3 -28.07 -3.626 16.479 1 17.86 ? C5 ADP 177 A 1 HETATM 22 C C6 ADP . . . C 3 -29.539 -3.409 16.494 1 13.99 ? C6 ADP 177 A 1 HETATM 23 N N6 ADP . . . C 3 -30.419 -4.063 17.282 1 22.93 ? N6 ADP 177 A 1 HETATM 24 N N1 ADP . . . C 3 -30.012 -2.471 15.632 1 21.78 ? N1 ADP 177 A 1 HETATM 25 C C2 ADP . . . C 3 -29.184 -1.734 14.89 1 18.23 ? C2 ADP 177 A 1 HETATM 26 N N3 ADP . . . C 3 -27.852 -1.876 14.743 1 20.83 ? N3 ADP 177 A 1 HETATM 27 C C4 ADP . . . C 3 -27.282 -2.803 15.556 1 20.02 ? C4 ADP 177 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #