data_1DAF # _model_server_result.job_id h7zANdI8OtEw02x1OeMnHA _model_server_result.datetime_utc '2024-12-04 15:30:57' _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 1daf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":226}' # _entry.id 1DAF # _exptl.entry_id 1DAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 107.1 _cell.angle_gamma 90 _cell.entry_id 1DAF _cell.length_a 73.2 _cell.length_b 49.2 _cell.length_c 61.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DAF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASP 54 A ASP 54 1_555 B CA CA . A CA 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc2 A OD2 ASP 54 A ASP 54 1_555 B CA CA . A CA 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc3 D O1A ADP . A ADP 226 1_555 B CA CA . A CA 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc4 B CA CA . A CA 227 1_555 E O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 B CA CA . A CA 227 1_555 E O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc6 B CA CA . A CA 227 1_555 E O HOH . A HOH 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc7 B CA CA . A CA 227 1_555 E O HOH . A HOH 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? # _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 1DAF _atom_sites.fract_transf_matrix[1][1] 0.013661 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004203 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020325 _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] 0.01693 _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 CA A 1 227 227 CA CA . C 3 DSD A 1 225 225 DSD DSD . D 4 ADP A 1 226 226 ADP ADP . E 5 HOH A 1 228 228 HOH HOH . E 5 HOH A 2 229 229 HOH HOH . E 5 HOH A 3 230 230 HOH HOH . E 5 HOH A 4 231 231 HOH HOH . E 5 HOH A 5 232 232 HOH HOH . E 5 HOH A 6 233 233 HOH HOH . E 5 HOH A 7 234 234 HOH HOH . E 5 HOH A 8 235 235 HOH HOH . E 5 HOH A 9 236 236 HOH HOH . E 5 HOH A 10 237 237 HOH HOH . E 5 HOH A 11 238 238 HOH HOH . E 5 HOH A 12 239 239 HOH HOH . E 5 HOH A 13 240 240 HOH HOH . E 5 HOH A 14 241 241 HOH HOH . E 5 HOH A 15 242 242 HOH HOH . E 5 HOH A 16 243 243 HOH HOH . E 5 HOH A 17 244 244 HOH HOH . E 5 HOH A 18 245 245 HOH HOH . E 5 HOH A 19 246 246 HOH HOH . E 5 HOH A 20 247 247 HOH HOH . E 5 HOH A 21 248 248 HOH HOH . E 5 HOH A 22 249 249 HOH HOH . E 5 HOH A 23 250 250 HOH HOH . E 5 HOH A 24 251 251 HOH HOH . E 5 HOH A 25 252 252 HOH HOH . E 5 HOH A 26 253 253 HOH HOH . E 5 HOH A 27 254 254 HOH HOH . E 5 HOH A 28 255 255 HOH HOH . E 5 HOH A 29 256 256 HOH HOH . E 5 HOH A 30 257 257 HOH HOH . E 5 HOH A 31 258 258 HOH HOH . E 5 HOH A 32 259 259 HOH HOH . E 5 HOH A 33 260 260 HOH HOH . E 5 HOH A 34 261 261 HOH HOH . E 5 HOH A 35 262 262 HOH HOH . E 5 HOH A 36 263 263 HOH HOH . E 5 HOH A 37 264 264 HOH HOH . E 5 HOH A 38 265 265 HOH HOH . E 5 HOH A 39 266 266 HOH HOH . E 5 HOH A 40 267 267 HOH HOH . E 5 HOH A 41 268 268 HOH HOH . E 5 HOH A 42 269 269 HOH HOH . E 5 HOH A 43 270 270 HOH HOH . E 5 HOH A 44 271 271 HOH HOH . E 5 HOH A 45 272 272 HOH HOH . E 5 HOH A 46 273 273 HOH HOH . E 5 HOH A 47 274 274 HOH HOH . E 5 HOH A 48 275 275 HOH HOH . E 5 HOH A 49 276 276 HOH HOH . E 5 HOH A 50 277 277 HOH HOH . E 5 HOH A 51 278 278 HOH HOH . E 5 HOH A 52 279 279 HOH HOH . E 5 HOH A 53 280 280 HOH HOH . E 5 HOH A 54 281 281 HOH HOH . E 5 HOH A 55 282 282 HOH HOH . E 5 HOH A 56 283 283 HOH HOH . E 5 HOH A 57 284 284 HOH HOH . E 5 HOH A 58 285 285 HOH HOH . E 5 HOH A 59 286 286 HOH HOH . E 5 HOH A 60 287 287 HOH HOH . E 5 HOH A 61 288 288 HOH HOH . E 5 HOH A 62 289 289 HOH HOH . E 5 HOH A 63 290 290 HOH HOH . E 5 HOH A 64 291 291 HOH HOH . E 5 HOH A 65 292 292 HOH HOH . E 5 HOH A 66 293 293 HOH HOH . E 5 HOH A 67 294 294 HOH HOH . E 5 HOH A 68 295 295 HOH HOH . E 5 HOH A 69 296 296 HOH HOH . E 5 HOH A 70 297 297 HOH HOH . E 5 HOH A 71 298 298 HOH HOH . E 5 HOH A 72 299 299 HOH HOH . E 5 HOH A 73 300 300 HOH HOH . E 5 HOH A 74 301 301 HOH HOH . E 5 HOH A 75 302 302 HOH HOH . E 5 HOH A 76 303 303 HOH HOH . E 5 HOH A 77 304 304 HOH HOH . E 5 HOH A 78 305 305 HOH HOH . E 5 HOH A 79 306 306 HOH HOH . E 5 HOH A 80 307 307 HOH HOH . E 5 HOH A 81 308 308 HOH HOH . E 5 HOH A 82 309 309 HOH HOH . E 5 HOH A 83 310 310 HOH HOH . E 5 HOH A 84 311 311 HOH HOH . E 5 HOH A 85 312 312 HOH HOH . E 5 HOH A 86 313 313 HOH HOH . E 5 HOH A 87 314 314 HOH HOH . E 5 HOH A 88 315 315 HOH HOH . E 5 HOH A 89 316 316 HOH HOH . E 5 HOH A 90 317 317 HOH HOH . E 5 HOH A 91 318 318 HOH HOH . E 5 HOH A 92 319 319 HOH HOH . E 5 HOH A 93 320 320 HOH HOH . E 5 HOH A 94 321 321 HOH HOH . E 5 HOH A 95 322 322 HOH HOH . E 5 HOH A 96 323 323 HOH HOH . E 5 HOH A 97 324 324 HOH HOH . E 5 HOH A 98 325 325 HOH HOH . E 5 HOH A 99 326 326 HOH HOH . E 5 HOH A 100 327 327 HOH HOH . E 5 HOH A 101 328 328 HOH HOH . E 5 HOH A 102 329 329 HOH HOH . E 5 HOH A 103 330 330 HOH HOH . E 5 HOH A 104 331 331 HOH HOH . E 5 HOH A 105 332 332 HOH HOH . E 5 HOH A 106 333 333 HOH HOH . E 5 HOH A 107 334 334 HOH HOH . E 5 HOH A 108 335 335 HOH HOH . E 5 HOH A 109 336 336 HOH HOH . E 5 HOH A 110 337 337 HOH HOH . E 5 HOH A 111 338 338 HOH HOH . E 5 HOH A 112 339 339 HOH HOH . E 5 HOH A 113 340 340 HOH HOH . E 5 HOH A 114 341 341 HOH HOH . E 5 HOH A 115 342 342 HOH HOH . E 5 HOH A 116 343 343 HOH HOH . E 5 HOH A 117 344 344 HOH HOH . E 5 HOH A 118 345 345 HOH HOH . E 5 HOH A 119 346 346 HOH HOH . E 5 HOH A 120 347 347 HOH HOH . E 5 HOH A 121 348 348 HOH HOH . E 5 HOH A 122 349 349 HOH HOH . E 5 HOH A 123 350 350 HOH HOH . E 5 HOH A 124 351 351 HOH HOH . E 5 HOH A 125 352 352 HOH HOH . E 5 HOH A 126 353 353 HOH HOH . E 5 HOH A 127 354 354 HOH HOH . E 5 HOH A 128 355 355 HOH HOH . E 5 HOH A 129 356 356 HOH HOH . E 5 HOH A 130 357 357 HOH HOH . E 5 HOH A 131 358 358 HOH HOH . E 5 HOH A 132 359 359 HOH HOH . E 5 HOH A 133 360 360 HOH HOH . E 5 HOH A 134 361 361 HOH HOH . E 5 HOH A 135 362 362 HOH HOH . E 5 HOH A 136 363 363 HOH HOH . E 5 HOH A 137 364 364 HOH HOH . E 5 HOH A 138 365 365 HOH HOH . E 5 HOH A 139 366 366 HOH HOH . E 5 HOH A 140 367 367 HOH HOH . E 5 HOH A 141 368 368 HOH HOH . E 5 HOH A 142 369 369 HOH HOH . E 5 HOH A 143 370 370 HOH HOH . E 5 HOH A 144 371 371 HOH HOH . E 5 HOH A 145 372 372 HOH HOH . E 5 HOH A 146 373 373 HOH HOH . E 5 HOH A 147 374 374 HOH HOH . E 5 HOH A 148 375 375 HOH HOH . E 5 HOH A 149 376 376 HOH HOH . E 5 HOH A 150 377 377 HOH HOH . E 5 HOH A 151 378 378 HOH HOH . E 5 HOH A 152 379 379 HOH HOH . E 5 HOH A 153 380 380 HOH HOH . E 5 HOH A 154 381 381 HOH HOH . E 5 HOH A 155 382 382 HOH HOH . E 5 HOH A 156 383 383 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 . . . D 4 3.701 23.155 11.416 1 18.76 ? PB ADP 226 A 1 HETATM 2 O O1B ADP . . . D 4 4.1 24.104 10.346 1 16.93 ? O1B ADP 226 A 1 HETATM 3 O O2B ADP . . . D 4 4.075 23.726 12.854 1 16.34 ? O2B ADP 226 A 1 HETATM 4 O O3B ADP . . . D 4 2.254 22.855 11.357 1 17.6 ? O3B ADP 226 A 1 HETATM 5 P PA ADP . . . D 4 5.305 20.765 12.009 1 17.4 ? PA ADP 226 A 1 HETATM 6 O O1A ADP . . . D 4 4.414 20.247 13.042 1 17.39 ? O1A ADP 226 A 1 HETATM 7 O O2A ADP . . . D 4 6.51 21.425 12.554 1 17.84 ? O2A ADP 226 A 1 HETATM 8 O O3A ADP . . . D 4 4.511 21.829 11.133 1 20.16 ? O3A ADP 226 A 1 HETATM 9 O O5' ADP . . . D 4 5.726 19.625 10.995 1 19.61 ? O5' ADP 226 A 1 HETATM 10 C C5' ADP . . . D 4 4.681 18.964 10.257 1 19.03 ? C5' ADP 226 A 1 HETATM 11 C C4' ADP . . . D 4 5.086 17.54 9.952 1 21.78 ? C4' ADP 226 A 1 HETATM 12 O O4' ADP . . . D 4 6.19 17.555 9.033 1 20.42 ? O4' ADP 226 A 1 HETATM 13 C C3' ADP . . . D 4 5.521 16.795 11.196 1 21.23 ? C3' ADP 226 A 1 HETATM 14 O O3' ADP . . . D 4 4.998 15.471 11.122 1 28.68 ? O3' ADP 226 A 1 HETATM 15 C C2' ADP . . . D 4 7.034 16.81 11.124 1 22.11 ? C2' ADP 226 A 1 HETATM 16 O O2' ADP . . . D 4 7.677 15.688 11.766 1 25.49 ? O2' ADP 226 A 1 HETATM 17 C C1' ADP . . . D 4 7.307 16.844 9.624 1 19.95 ? C1' ADP 226 A 1 HETATM 18 N N9 ADP . . . D 4 8.564 17.585 9.305 1 19.47 ? N9 ADP 226 A 1 HETATM 19 C C8 ADP . . . D 4 8.712 18.933 9.422 1 17.74 ? C8 ADP 226 A 1 HETATM 20 N N7 ADP . . . D 4 9.984 19.223 9.195 1 17.24 ? N7 ADP 226 A 1 HETATM 21 C C5 ADP . . . D 4 10.636 18.111 8.937 1 17.66 ? C5 ADP 226 A 1 HETATM 22 C C6 ADP . . . D 4 11.957 17.82 8.638 1 19.05 ? C6 ADP 226 A 1 HETATM 23 N N6 ADP . . . D 4 12.858 18.771 8.521 1 14.89 ? N6 ADP 226 A 1 HETATM 24 N N1 ADP . . . D 4 12.329 16.526 8.404 1 18.73 ? N1 ADP 226 A 1 HETATM 25 C C2 ADP . . . D 4 11.4 15.535 8.458 1 20.24 ? C2 ADP 226 A 1 HETATM 26 N N3 ADP . . . D 4 10.129 15.804 8.754 1 20.54 ? N3 ADP 226 A 1 HETATM 27 C C4 ADP . . . D 4 9.715 17.059 8.993 1 19.62 ? C4 ADP 226 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #