data_1DAF # _model_server_result.job_id V5HCecPMvTO-GfztH5r38A _model_server_result.datetime_utc '2024-12-04 15:29:44' _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 1daf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":225}' # _entry.id 1DAF # _exptl.entry_id 1DAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 232.277 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID' _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 3 _struct_asym.id C _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 H20 N2 O4' _chem_comp.formula_weight 232.277 _chem_comp.id DSD _chem_comp.mon_nstd_flag . _chem_comp.name '7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID' _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 C1 O1 DSD doub 127 n n C1 O2 DSD sing 128 n n C1 C2 DSD sing 129 n n O2 HO2 DSD sing 130 n n C2 C3 DSD sing 131 n n C2 H21 DSD sing 132 n n C2 H22 DSD sing 133 n n C3 C4 DSD sing 134 n n C3 H31 DSD sing 135 n n C3 H32 DSD sing 136 n n C4 C5 DSD sing 137 n n C4 H41 DSD sing 138 n n C4 H42 DSD sing 139 n n C5 C6 DSD sing 140 n n C5 H51 DSD sing 141 n n C5 H52 DSD sing 142 n n C6 C7 DSD sing 143 n n C6 H61 DSD sing 144 n n C6 H62 DSD sing 145 n n C7 C8 DSD sing 146 n n C7 N7 DSD sing 147 n n C7 H7 DSD sing 148 n n C8 C9 DSD sing 149 n n C8 N8 DSD sing 150 n n C8 H8 DSD sing 151 n n C9 H91 DSD sing 152 n n C9 H92 DSD sing 153 n n C9 H93 DSD sing 154 n n N7 C DSD sing 155 n n N7 HN7 DSD sing 156 n n C O DSD doub 157 n n C OXT DSD sing 158 n n OXT HXT DSD sing 159 n n N8 HN81 DSD sing 160 n n N8 HN82 DSD sing 161 n n # _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 C C1 DSD . . . C 3 -6.641 28.169 7.056 1 21.67 ? C1 DSD 225 A 1 HETATM 2 O O1 DSD . . . C 3 -7.405 27.488 6.352 1 17.95 ? O1 DSD 225 A 1 HETATM 3 O O2 DSD . . . C 3 -5.869 28.999 6.579 1 19.24 ? O2 DSD 225 A 1 HETATM 4 C C2 DSD . . . C 3 -6.586 27.969 8.567 1 20.61 ? C2 DSD 225 A 1 HETATM 5 C C3 DSD . . . C 3 -5.783 26.74 8.947 1 23.35 ? C3 DSD 225 A 1 HETATM 6 C C4 DSD . . . C 3 -5.691 26.501 10.441 1 26.4 ? C4 DSD 225 A 1 HETATM 7 C C5 DSD . . . C 3 -4.585 25.489 10.693 1 30.41 ? C5 DSD 225 A 1 HETATM 8 C C6 DSD . . . C 3 -4.504 25.165 12.17 1 34.59 ? C6 DSD 225 A 1 HETATM 9 C C7 DSD . . . C 3 -3.272 24.398 12.662 1 35.47 ? C7 DSD 225 A 1 HETATM 10 C C8 DSD . . . C 3 -3.274 22.936 12.149 1 35.76 ? C8 DSD 225 A 1 HETATM 11 C C9 DSD . . . C 3 -4.481 22.157 12.673 1 35.81 ? C9 DSD 225 A 1 HETATM 12 N N7 DSD . . . C 3 -3.301 24.438 14.125 1 35.31 ? N7 DSD 225 A 1 HETATM 13 C C DSD . . . C 3 -2.209 24.697 14.872 1 36.01 ? C DSD 225 A 1 HETATM 14 O O DSD . . . C 3 -1.196 25.185 14.373 1 30.15 ? O DSD 225 A 1 HETATM 15 O OXT DSD . . . C 3 -2.279 24.481 16.077 1 33.4 ? OXT DSD 225 A 1 HETATM 16 N N8 DSD . . . C 3 -2.034 22.344 12.642 1 37.23 ? N8 DSD 225 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #