data_3JU9 # _model_server_result.job_id dHSrAC025p70XOjbDiCspQ _model_server_result.datetime_utc '2024-11-24 17:48:13' _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 3ju9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":238}' # _entry.id 3JU9 # _exptl.entry_id 3JU9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 103.12 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'D-ALPHA-AMINOBUTYRIC 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 90 _cell.angle_gamma 90 _cell.entry_id 3JU9 _cell.length_a 68.323 _cell.length_b 73.02 _cell.length_c 99.542 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JU9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # 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 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OE2 GLU 8 A GLU 8 1_555 E MN MN . A MN 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 D CA CA . A CA 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 D CA CA . A CA 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc4 A OD2 ASP 10 A ASP 10 1_555 E MN MN . A MN 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc5 A O TYR 12 A TYR 12 1_555 D CA CA . A CA 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 D CA CA . A CA 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc7 A OD2 ASP 19 A ASP 19 1_555 D CA CA . A CA 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc8 A OD1 ASP 19 A ASP 19 1_555 E MN MN . A MN 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc9 A NE2 HIS 24 A HIS 24 1_555 E MN MN . A MN 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc10 D CA CA . A CA 240 1_555 H O HOH . A HOH 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc11 D CA CA . A CA 240 1_555 H O HOH . A HOH 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc12 E MN MN . A MN 241 1_555 H O HOH . A HOH 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc13 E MN MN . A MN 241 1_555 H O HOH . A HOH 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? # _chem_comp.formula 'C4 H9 N O2' _chem_comp.formula_weight 103.12 _chem_comp.id DBB _chem_comp.mon_nstd_flag . _chem_comp.name 'D-ALPHA-AMINOBUTYRIC ACID' _chem_comp.type 'd-peptide linking' _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 N CA DBB sing 70 n n CA C DBB sing 71 n n CA CB DBB sing 72 n n C O DBB doub 73 n n CB CG DBB sing 74 n n C OXT DBB sing 75 n n N H DBB sing 76 n n N H2 DBB sing 77 n n CA HA DBB sing 78 n n CB HB2 DBB sing 79 n n CB HB3 DBB sing 80 n n CG HG1 DBB sing 81 n n CG HG2 DBB sing 82 n n CG HG3 DBB sing 83 n n OXT HXT DBB sing 84 n n # _atom_sites.entry_id 3JU9 _atom_sites.fract_transf_matrix[1][1] 0.014636 _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] 0.013695 _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] 0.010046 _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 DBB A 1 238 238 DBB DBB . C 3 GOL A 1 239 239 GOL GOL . D 4 CA A 1 240 240 CA CA . E 5 MN A 1 241 241 MN MN . F 6 CL A 1 242 242 CL CL . G 6 CL A 1 243 243 CL CL . H 7 HOH A 1 244 244 HOH HOH . H 7 HOH A 2 245 245 HOH HOH . H 7 HOH A 3 246 246 HOH HOH . H 7 HOH A 4 247 247 HOH HOH . H 7 HOH A 5 248 248 HOH HOH . H 7 HOH A 6 249 249 HOH HOH . H 7 HOH A 7 250 250 HOH HOH . H 7 HOH A 8 251 251 HOH HOH . H 7 HOH A 9 252 252 HOH HOH . H 7 HOH A 10 253 253 HOH HOH . H 7 HOH A 11 254 254 HOH HOH . H 7 HOH A 12 255 255 HOH HOH . H 7 HOH A 13 256 256 HOH HOH . H 7 HOH A 14 257 257 HOH HOH . H 7 HOH A 15 258 258 HOH HOH . H 7 HOH A 16 259 259 HOH HOH . H 7 HOH A 17 260 260 HOH HOH . H 7 HOH A 18 261 261 HOH HOH . H 7 HOH A 19 262 262 HOH HOH . H 7 HOH A 20 263 263 HOH HOH . H 7 HOH A 21 264 264 HOH HOH . H 7 HOH A 22 265 265 HOH HOH . H 7 HOH A 23 266 266 HOH HOH . H 7 HOH A 24 267 267 HOH HOH . H 7 HOH A 25 268 268 HOH HOH . H 7 HOH A 26 269 269 HOH HOH . H 7 HOH A 27 270 270 HOH HOH . H 7 HOH A 28 271 271 HOH HOH . H 7 HOH A 29 272 272 HOH HOH . H 7 HOH A 30 273 273 HOH HOH . H 7 HOH A 31 274 274 HOH HOH . H 7 HOH A 32 275 275 HOH HOH . H 7 HOH A 33 276 276 HOH HOH . H 7 HOH A 34 277 277 HOH HOH . H 7 HOH A 35 278 278 HOH HOH . H 7 HOH A 36 279 279 HOH HOH . H 7 HOH A 37 280 280 HOH HOH . H 7 HOH A 38 281 281 HOH HOH . H 7 HOH A 39 282 282 HOH HOH . H 7 HOH A 40 283 283 HOH HOH . H 7 HOH A 41 284 284 HOH HOH . H 7 HOH A 42 285 285 HOH HOH . H 7 HOH A 43 286 286 HOH HOH . H 7 HOH A 44 287 287 HOH HOH . H 7 HOH A 45 288 288 HOH HOH . H 7 HOH A 46 289 289 HOH HOH . H 7 HOH A 47 290 290 HOH HOH . H 7 HOH A 48 291 291 HOH HOH . H 7 HOH A 49 292 292 HOH HOH . H 7 HOH A 50 293 293 HOH HOH . H 7 HOH A 51 294 294 HOH HOH . H 7 HOH A 52 295 295 HOH HOH . H 7 HOH A 53 296 296 HOH HOH . H 7 HOH A 54 297 297 HOH HOH . H 7 HOH A 55 298 298 HOH HOH . H 7 HOH A 56 299 299 HOH HOH . H 7 HOH A 57 300 300 HOH HOH . H 7 HOH A 58 301 301 HOH HOH . H 7 HOH A 59 302 302 HOH HOH . H 7 HOH A 60 303 303 HOH HOH . H 7 HOH A 61 304 304 HOH HOH . H 7 HOH A 62 305 305 HOH HOH . H 7 HOH A 63 306 306 HOH HOH . H 7 HOH A 64 307 307 HOH HOH . H 7 HOH A 65 308 308 HOH HOH . H 7 HOH A 66 309 309 HOH HOH . H 7 HOH A 67 310 310 HOH HOH . H 7 HOH A 68 311 311 HOH HOH . H 7 HOH A 69 312 312 HOH HOH . H 7 HOH A 70 313 313 HOH HOH . H 7 HOH A 71 314 314 HOH HOH . H 7 HOH A 72 315 315 HOH HOH . H 7 HOH A 73 316 316 HOH HOH . H 7 HOH A 74 317 317 HOH HOH . H 7 HOH A 75 318 318 HOH HOH . H 7 HOH A 76 319 319 HOH HOH . H 7 HOH A 77 320 320 HOH HOH . H 7 HOH A 78 321 321 HOH HOH . H 7 HOH A 79 322 322 HOH HOH . H 7 HOH A 80 323 323 HOH HOH . H 7 HOH A 81 324 324 HOH HOH . H 7 HOH A 82 325 325 HOH HOH . H 7 HOH A 83 326 326 HOH HOH . H 7 HOH A 84 327 327 HOH HOH . H 7 HOH A 85 328 328 HOH HOH . H 7 HOH A 86 329 329 HOH HOH . H 7 HOH A 87 330 330 HOH HOH . H 7 HOH A 88 331 331 HOH HOH . H 7 HOH A 89 332 332 HOH HOH . H 7 HOH A 90 333 333 HOH HOH . H 7 HOH A 91 334 334 HOH HOH . H 7 HOH A 92 335 335 HOH HOH . H 7 HOH A 93 336 336 HOH HOH . H 7 HOH A 94 337 337 HOH HOH . H 7 HOH A 95 338 338 HOH HOH . H 7 HOH A 96 339 339 HOH HOH . H 7 HOH A 97 340 340 HOH HOH . H 7 HOH A 98 341 341 HOH HOH . H 7 HOH A 99 342 342 HOH HOH . H 7 HOH A 100 343 343 HOH HOH . H 7 HOH A 101 344 344 HOH HOH . H 7 HOH A 102 345 345 HOH HOH . H 7 HOH A 103 346 346 HOH HOH . H 7 HOH A 104 347 347 HOH HOH . H 7 HOH A 105 348 348 HOH HOH . H 7 HOH A 106 349 349 HOH HOH . H 7 HOH A 107 350 350 HOH HOH . H 7 HOH A 108 351 351 HOH HOH . H 7 HOH A 109 352 352 HOH HOH . H 7 HOH A 110 353 353 HOH HOH . H 7 HOH A 111 354 354 HOH HOH . H 7 HOH A 112 355 355 HOH HOH . H 7 HOH A 113 356 356 HOH HOH . H 7 HOH A 114 357 357 HOH HOH . H 7 HOH A 115 358 358 HOH HOH . H 7 HOH A 116 359 359 HOH HOH . H 7 HOH A 117 360 360 HOH HOH . H 7 HOH A 118 361 361 HOH HOH . H 7 HOH A 119 362 362 HOH HOH . H 7 HOH A 120 363 363 HOH HOH . H 7 HOH A 121 364 364 HOH HOH . H 7 HOH A 122 365 365 HOH HOH . H 7 HOH A 123 366 366 HOH HOH . H 7 HOH A 124 367 367 HOH HOH . H 7 HOH A 125 368 368 HOH HOH . H 7 HOH A 126 369 369 HOH HOH . H 7 HOH A 127 370 370 HOH HOH . H 7 HOH A 128 371 371 HOH HOH . H 7 HOH A 129 372 372 HOH HOH . H 7 HOH A 130 373 373 HOH HOH . H 7 HOH A 131 374 374 HOH HOH . H 7 HOH A 132 375 375 HOH HOH . H 7 HOH A 133 376 376 HOH HOH . H 7 HOH A 134 377 377 HOH HOH . H 7 HOH A 135 378 378 HOH HOH . H 7 HOH A 136 379 379 HOH HOH . H 7 HOH A 137 380 380 HOH HOH . H 7 HOH A 138 381 381 HOH HOH . H 7 HOH A 139 382 382 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 N N DBB . . . B 2 13.479 5.779 -5.064 1 33.09 ? N DBB 238 A 1 HETATM 2 C CA DBB . . . B 2 12.488 5.426 -6.164 1 34.84 ? CA DBB 238 A 1 HETATM 3 C C DBB . . . B 2 12.71 4.29 -7.156 1 35.28 ? C DBB 238 A 1 HETATM 4 O O DBB . . . B 2 11.771 3.53 -7.436 1 36.1 ? O DBB 238 A 1 HETATM 5 C CB DBB . . . B 2 11.074 5.894 -5.892 1 34.06 ? CB DBB 238 A 1 HETATM 6 C CG DBB . . . B 2 10.97 7.408 -5.615 1 32.34 ? CG DBB 238 A 1 HETATM 7 O OXT DBB . . . B 2 13.822 4.157 -7.717 1 34.5 ? OXT DBB 238 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 7 #