data_2TDT # _model_server_result.job_id C2GQa8nF9SGGshaYViiaZw _model_server_result.datetime_utc '2024-12-22 03:09:30' _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 2tdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":281}' # _entry.id 2TDT # _exptl.entry_id 2TDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.182 _entity.id 3 _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 2TDT _cell.length_a 95.71 _cell.length_b 95.71 _cell.length_c 72.79 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2TDT _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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 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 # _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 323 n n CA C NPI sing 324 n n CA N NPI sing 325 n n CA HA NPI sing 326 n n CB C4 NPI sing 327 n n CB H31 NPI sing 328 n n CB H32 NPI sing 329 n n C4 C5 NPI sing 330 n n C4 H41 NPI sing 331 n n C4 H42 NPI sing 332 n n C5 C6 NPI sing 333 n n C5 H51 NPI sing 334 n n C5 H52 NPI sing 335 n n C6 C7 NPI sing 336 n n C6 H61 NPI sing 337 n n C6 H62 NPI sing 338 n n C O NPI doub 339 n n C OXT NPI sing 340 n n OXT HXT NPI sing 341 n n N H NPI sing 342 n n N H2 NPI sing 343 n n C7 O71 NPI doub 344 n n C7 O72 NPI sing 345 n n O72 HO NPI sing 346 n n # _atom_sites.entry_id 2TDT _atom_sites.fract_transf_matrix[1][1] 0.010448 _atom_sites.fract_transf_matrix[1][2] 0.006032 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012065 _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] 0.013738 _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 COA A 1 280 280 COA COA . C 3 NPI A 1 281 281 NPI NPI . D 4 HOH A 1 301 301 HOH HOH . D 4 HOH A 2 302 302 HOH HOH . D 4 HOH A 3 303 303 HOH HOH . D 4 HOH A 4 304 304 HOH HOH . D 4 HOH A 5 305 305 HOH HOH . D 4 HOH A 6 306 306 HOH HOH . D 4 HOH A 7 307 307 HOH HOH . D 4 HOH A 8 308 308 HOH HOH . D 4 HOH A 9 309 309 HOH HOH . D 4 HOH A 10 310 310 HOH HOH . D 4 HOH A 11 311 311 HOH HOH . D 4 HOH A 12 312 312 HOH HOH . D 4 HOH A 13 313 313 HOH HOH . D 4 HOH A 14 314 314 HOH HOH . D 4 HOH A 15 315 315 HOH HOH . D 4 HOH A 16 316 316 HOH HOH . D 4 HOH A 17 317 317 HOH HOH . D 4 HOH A 18 318 318 HOH HOH . D 4 HOH A 19 319 319 HOH HOH . D 4 HOH A 20 320 320 HOH HOH . D 4 HOH A 21 321 321 HOH HOH . D 4 HOH A 22 322 322 HOH HOH . D 4 HOH A 23 323 323 HOH HOH . D 4 HOH A 24 324 324 HOH HOH . D 4 HOH A 25 325 325 HOH HOH . D 4 HOH A 26 326 326 HOH HOH . D 4 HOH A 27 327 327 HOH HOH . D 4 HOH A 28 328 328 HOH HOH . D 4 HOH A 29 329 329 HOH HOH . D 4 HOH A 30 330 330 HOH HOH . D 4 HOH A 31 331 331 HOH HOH . D 4 HOH A 32 332 332 HOH HOH . D 4 HOH A 33 333 333 HOH HOH . D 4 HOH A 34 334 334 HOH HOH . D 4 HOH A 35 335 335 HOH HOH . D 4 HOH A 36 336 336 HOH HOH . D 4 HOH A 37 337 337 HOH HOH . D 4 HOH A 38 338 338 HOH HOH . D 4 HOH A 39 339 339 HOH HOH . D 4 HOH A 40 340 340 HOH HOH . D 4 HOH A 41 341 341 HOH HOH . D 4 HOH A 42 342 342 HOH HOH . D 4 HOH A 43 343 343 HOH HOH . D 4 HOH A 44 344 344 HOH HOH . D 4 HOH A 45 345 345 HOH HOH . D 4 HOH A 46 346 346 HOH HOH . D 4 HOH A 47 347 347 HOH HOH . D 4 HOH A 48 348 348 HOH HOH . D 4 HOH A 49 349 349 HOH HOH . D 4 HOH A 50 350 350 HOH HOH . D 4 HOH A 51 351 351 HOH HOH . D 4 HOH A 52 352 352 HOH HOH . D 4 HOH A 53 353 353 HOH HOH . D 4 HOH A 54 354 354 HOH HOH . D 4 HOH A 55 355 355 HOH HOH . D 4 HOH A 56 356 356 HOH HOH . D 4 HOH A 57 357 357 HOH HOH . D 4 HOH A 58 358 358 HOH HOH . D 4 HOH A 59 359 359 HOH HOH . D 4 HOH A 60 360 360 HOH HOH . D 4 HOH A 61 361 361 HOH HOH . D 4 HOH A 62 362 362 HOH HOH . D 4 HOH A 63 363 363 HOH HOH . D 4 HOH A 64 364 364 HOH HOH . D 4 HOH A 65 365 365 HOH HOH . D 4 HOH A 66 366 366 HOH HOH . D 4 HOH A 67 367 367 HOH HOH . D 4 HOH A 68 368 368 HOH HOH . D 4 HOH A 69 369 369 HOH HOH . D 4 HOH A 70 370 370 HOH HOH . D 4 HOH A 71 371 371 HOH HOH . D 4 HOH A 72 372 372 HOH HOH . D 4 HOH A 73 373 373 HOH HOH . D 4 HOH A 74 374 374 HOH HOH . D 4 HOH A 75 375 375 HOH HOH . D 4 HOH A 76 376 376 HOH HOH . D 4 HOH A 77 377 377 HOH HOH . D 4 HOH A 78 378 378 HOH HOH . D 4 HOH A 79 379 379 HOH HOH . D 4 HOH A 80 380 380 HOH HOH . D 4 HOH A 81 381 381 HOH HOH . D 4 HOH A 82 382 382 HOH HOH . D 4 HOH A 83 383 383 HOH HOH . D 4 HOH A 84 384 384 HOH HOH . D 4 HOH A 85 385 385 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 . . . C 3 13.244 4.614 1.262 1 13.09 ? CA NPI 281 A 1 HETATM 2 C CB NPI . . . C 3 13.418 5.754 0.304 1 9.87 ? CB NPI 281 A 1 HETATM 3 C C4 NPI . . . C 3 13.904 5.216 -1.008 1 6.33 ? C4 NPI 281 A 1 HETATM 4 C C5 NPI . . . C 3 13.994 6.334 -2.069 1 16.85 ? C5 NPI 281 A 1 HETATM 5 C C6 NPI . . . C 3 14.395 5.872 -3.454 1 17.91 ? C6 NPI 281 A 1 HETATM 6 C C NPI . . . C 3 14.543 3.802 1.276 1 12.22 ? C NPI 281 A 1 HETATM 7 O O NPI . . . C 3 15.515 4.245 2.034 1 12.06 ? O NPI 281 A 1 HETATM 8 O OXT NPI . . . C 3 14.669 2.771 0.602 1 13.37 ? OXT NPI 281 A 1 HETATM 9 N N NPI . . . C 3 12.917 5.107 2.602 1 8.99 ? N NPI 281 A 1 HETATM 10 C C7 NPI . . . C 3 14.398 6.925 -4.581 1 14.16 ? C7 NPI 281 A 1 HETATM 11 O O71 NPI . . . C 3 14.232 6.63 -5.774 1 23.39 ? O71 NPI 281 A 1 HETATM 12 O O72 NPI . . . C 3 14.613 8.205 -4.415 1 21.05 ? O72 NPI 281 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 12 #