data_1KGQ # _model_server_result.job_id FnqIb2uFHQ8TJWPRyVQtXw _model_server_result.datetime_utc '2025-08-31 02:33:58' _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 1kgq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 1KGQ # _exptl.entry_id 1KGQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-aminoheptanedioic 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 120 _cell.entry_id 1KGQ _cell.length_a 95.84 _cell.length_b 95.84 _cell.length_c 72.64 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KGQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 143.76 82.999875 0 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 165.999749 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 # _chem_comp.formula 'C7 H13 N O4' _chem_comp.formula_weight 175.182 _chem_comp.id NPI _chem_comp.mon_nstd_flag n _chem_comp.name '(2S)-2-aminoheptanedioic acid' _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms 'L-2-AMINOPIMELIC ACID' # 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 CA CB NPI sing 237 n n CA C NPI sing 238 n n CA N NPI sing 239 n n CA HA NPI sing 240 n n CB C4 NPI sing 241 n n CB H31 NPI sing 242 n n CB H32 NPI sing 243 n n C4 C5 NPI sing 244 n n C4 H41 NPI sing 245 n n C4 H42 NPI sing 246 n n C5 C6 NPI sing 247 n n C5 H51 NPI sing 248 n n C5 H52 NPI sing 249 n n C6 C7 NPI sing 250 n n C6 H61 NPI sing 251 n n C6 H62 NPI sing 252 n n C O NPI doub 253 n n C OXT NPI sing 254 n n OXT HXT NPI sing 255 n n N H NPI sing 256 n n N H2 NPI sing 257 n n C7 O71 NPI doub 258 n n C7 O72 NPI sing 259 n n O72 HO NPI sing 260 n n # _atom_sites.entry_id 1KGQ _atom_sites.fract_transf_matrix[1][1] 0.010434 _atom_sites.fract_transf_matrix[1][2] 0.006024 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012048 _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] 0.013767 _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 NPI A 1 301 1 NPI 2AP . C 3 SCO A 1 302 2 SCO ASC . D 4 HOH A 1 303 1 HOH HOH . D 4 HOH A 2 304 2 HOH HOH . D 4 HOH A 3 305 3 HOH HOH . D 4 HOH A 4 306 4 HOH HOH . D 4 HOH A 5 307 5 HOH HOH . D 4 HOH A 6 308 6 HOH HOH . D 4 HOH A 7 309 7 HOH HOH . D 4 HOH A 8 310 9 HOH HOH . D 4 HOH A 9 311 10 HOH HOH . D 4 HOH A 10 312 11 HOH HOH . D 4 HOH A 11 313 12 HOH HOH . D 4 HOH A 12 314 13 HOH HOH . D 4 HOH A 13 315 14 HOH HOH . D 4 HOH A 14 316 15 HOH HOH . D 4 HOH A 15 317 16 HOH HOH . D 4 HOH A 16 318 17 HOH HOH . D 4 HOH A 17 319 18 HOH HOH . D 4 HOH A 18 320 19 HOH HOH . D 4 HOH A 19 321 20 HOH HOH . D 4 HOH A 20 322 21 HOH HOH . D 4 HOH A 21 323 22 HOH HOH . D 4 HOH A 22 324 23 HOH HOH . D 4 HOH A 23 325 24 HOH HOH . D 4 HOH A 24 326 25 HOH HOH . D 4 HOH A 25 327 26 HOH HOH . D 4 HOH A 26 328 28 HOH HOH . D 4 HOH A 27 329 29 HOH HOH . D 4 HOH A 28 330 30 HOH HOH . D 4 HOH A 29 331 31 HOH HOH . D 4 HOH A 30 332 32 HOH HOH . D 4 HOH A 31 333 33 HOH HOH . D 4 HOH A 32 334 34 HOH HOH . D 4 HOH A 33 335 35 HOH HOH . D 4 HOH A 34 336 36 HOH HOH . D 4 HOH A 35 337 37 HOH HOH . D 4 HOH A 36 338 38 HOH HOH . D 4 HOH A 37 339 39 HOH HOH . D 4 HOH A 38 340 40 HOH HOH . D 4 HOH A 39 341 41 HOH HOH . D 4 HOH A 40 342 42 HOH HOH . D 4 HOH A 41 343 43 HOH HOH . D 4 HOH A 42 344 45 HOH HOH . D 4 HOH A 43 345 46 HOH HOH . D 4 HOH A 44 346 47 HOH HOH . D 4 HOH A 45 347 48 HOH HOH . D 4 HOH A 46 348 49 HOH HOH . D 4 HOH A 47 349 50 HOH HOH . D 4 HOH A 48 350 51 HOH HOH . D 4 HOH A 49 351 52 HOH HOH . D 4 HOH A 50 352 54 HOH HOH . D 4 HOH A 51 353 56 HOH HOH . D 4 HOH A 52 354 57 HOH HOH . D 4 HOH A 53 355 58 HOH HOH . D 4 HOH A 54 356 59 HOH HOH . D 4 HOH A 55 357 60 HOH HOH . D 4 HOH A 56 358 61 HOH HOH . D 4 HOH A 57 359 62 HOH HOH . D 4 HOH A 58 360 63 HOH HOH . D 4 HOH A 59 361 64 HOH HOH . D 4 HOH A 60 362 65 HOH HOH . D 4 HOH A 61 363 67 HOH HOH . D 4 HOH A 62 364 68 HOH HOH . D 4 HOH A 63 365 71 HOH HOH . D 4 HOH A 64 366 72 HOH HOH . D 4 HOH A 65 367 73 HOH HOH . D 4 HOH A 66 368 75 HOH HOH . D 4 HOH A 67 369 76 HOH HOH . D 4 HOH A 68 370 79 HOH HOH . D 4 HOH A 69 371 80 HOH HOH . D 4 HOH A 70 372 81 HOH HOH . D 4 HOH A 71 373 82 HOH HOH . D 4 HOH A 72 374 86 HOH HOH . D 4 HOH A 73 375 89 HOH HOH . D 4 HOH A 74 376 90 HOH HOH . D 4 HOH A 75 377 91 HOH HOH . D 4 HOH A 76 378 92 HOH HOH . D 4 HOH A 77 379 93 HOH HOH . D 4 HOH A 78 380 96 HOH HOH . D 4 HOH A 79 381 97 HOH HOH . D 4 HOH A 80 382 99 HOH HOH . D 4 HOH A 81 383 100 HOH HOH . D 4 HOH A 82 384 101 HOH HOH . D 4 HOH A 83 385 102 HOH HOH . D 4 HOH A 84 386 103 HOH HOH . D 4 HOH A 85 387 104 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 CA NPI . . . B 2 61.255 87.63 1.28 1 12.39 ? CA NPI 301 A 1 HETATM 2 C CB NPI . . . B 2 61.32 88.769 0.262 1 10.41 ? CB NPI 301 A 1 HETATM 3 C C4 NPI . . . B 2 61.762 88.318 -1.121 1 6.91 ? C4 NPI 301 A 1 HETATM 4 C C5 NPI . . . B 2 62.033 89.457 -2.119 1 15.18 ? C5 NPI 301 A 1 HETATM 5 C C6 NPI . . . B 2 62.311 88.96 -3.528 1 17.65 ? C6 NPI 301 A 1 HETATM 6 C C NPI . . . B 2 62.566 86.821 1.322 1 15.12 ? C NPI 301 A 1 HETATM 7 O O NPI . . . B 2 63.555 87.233 2.059 1 11.28 ? O NPI 301 A 1 HETATM 8 O OXT NPI . . . B 2 62.727 85.793 0.681 1 14.91 ? OXT NPI 301 A 1 HETATM 9 N N NPI . . . B 2 60.952 88.098 2.639 1 5.3 ? N NPI 301 A 1 HETATM 10 C C7 NPI . . . B 2 62.407 90.02 -4.605 1 11.04 ? C7 NPI 301 A 1 HETATM 11 O O71 NPI . . . B 2 62.331 89.734 -5.798 1 22.52 ? O71 NPI 301 A 1 HETATM 12 O O72 NPI . . . B 2 62.587 91.28 -4.334 1 22.33 ? O72 NPI 301 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 413 _model_server_stats.encode_time_ms 52 _model_server_stats.element_count 12 #