data_5N8T # _model_server_result.job_id 3HnGOYtKS_EwEF0udoGxaQ _model_server_result.datetime_utc '2025-01-13 18:23:42' _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 5n8t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":209}' # _entry.id 5N8T # _exptl.entry_id 5N8T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.188 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-LYSINE _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 5N8T _cell.length_a 57.779 _cell.length_b 57.779 _cell.length_c 84.405 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N8T _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id J _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 covale ? covale1 B C DLE . A DLE 201 1_555 C N DTR . A DTR 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 C C DTR . A DTR 202 1_555 D N DGN . A DGN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale3 D C DGN . A DGN 203 1_555 E N DHI . A DHI 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale4 E C DHI . A DHI 204 1_555 F N DGL . A DGL 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 F C DGL . A DGL 205 1_555 G N DAL . A DAL 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 G C DAL . A DAL 206 1_555 H N DTH . A DTH 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale7 H C DTH . A DTH 207 1_555 I N DTR . A DTR 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale8 I C DTR . A DTR 208 1_555 J N DLY . A DLY 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? # _chem_comp.formula 'C6 H14 N2 O2' _chem_comp.formula_weight 146.188 _chem_comp.id DLY _chem_comp.mon_nstd_flag . _chem_comp.name D-LYSINE _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 DLY sing 161 n n N H DLY sing 162 n n N H2 DLY sing 163 n n CA C DLY sing 164 n n CA CB DLY sing 165 n n CA HA DLY sing 166 n n C O DLY doub 167 n n C OXT DLY sing 168 n n CB CG DLY sing 169 n n CB HB2 DLY sing 170 n n CB HB3 DLY sing 171 n n CG CD DLY sing 172 n n CG HG2 DLY sing 173 n n CG HG3 DLY sing 174 n n CD CE DLY sing 175 n n CD HD2 DLY sing 176 n n CD HD3 DLY sing 177 n n CE NZ DLY sing 178 n n CE HE2 DLY sing 179 n n CE HE3 DLY sing 180 n n NZ HZ1 DLY sing 181 n n NZ HZ2 DLY sing 182 n n OXT HXT DLY sing 183 n n # _atom_sites.entry_id 5N8T _atom_sites.fract_transf_matrix[1][1] 0.017307 _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] 0.017307 _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] 0.011848 _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 DLE A 1 201 3 DLE DLE . C 3 DTR A 1 202 4 DTR DTR . D 4 DGN A 1 203 5 DGN DGN . E 5 DHI A 1 204 6 DHI DHI . F 6 DGL A 1 205 7 DGL DGL . G 7 DAL A 1 206 8 DAL DAL . H 8 DTH A 1 207 9 DTH DTH . I 3 DTR A 1 208 10 DTR DTR . J 9 DLY A 1 209 11 DLY DLY . K 10 HOH A 1 301 99 HOH HOH . K 10 HOH A 2 302 29 HOH HOH . K 10 HOH A 3 303 21 HOH HOH . K 10 HOH A 4 304 35 HOH HOH . K 10 HOH A 5 305 14 HOH HOH . K 10 HOH A 6 306 24 HOH HOH . K 10 HOH A 7 307 101 HOH HOH . K 10 HOH A 8 308 1 HOH HOH . K 10 HOH A 9 309 45 HOH HOH . K 10 HOH A 10 310 12 HOH HOH . K 10 HOH A 11 311 26 HOH HOH . K 10 HOH A 12 312 59 HOH HOH . K 10 HOH A 13 313 107 HOH HOH . K 10 HOH A 14 314 72 HOH HOH . K 10 HOH A 15 315 38 HOH HOH . K 10 HOH A 16 316 22 HOH HOH . K 10 HOH A 17 317 8 HOH HOH . K 10 HOH A 18 318 13 HOH HOH . K 10 HOH A 19 319 60 HOH HOH . K 10 HOH A 20 320 108 HOH HOH . K 10 HOH A 21 321 82 HOH HOH . K 10 HOH A 22 322 106 HOH HOH . K 10 HOH A 23 323 65 HOH HOH . K 10 HOH A 24 324 39 HOH HOH . K 10 HOH A 25 325 34 HOH HOH . K 10 HOH A 26 326 7 HOH HOH . K 10 HOH A 27 327 102 HOH HOH . K 10 HOH A 28 328 5 HOH HOH . K 10 HOH A 29 329 103 HOH HOH . K 10 HOH A 30 330 31 HOH HOH . K 10 HOH A 31 331 40 HOH HOH . K 10 HOH A 32 332 41 HOH HOH . K 10 HOH A 33 333 2 HOH HOH . K 10 HOH A 34 334 100 HOH HOH . K 10 HOH A 35 335 69 HOH HOH . K 10 HOH A 36 336 73 HOH HOH . K 10 HOH A 37 337 105 HOH HOH . K 10 HOH A 38 338 32 HOH HOH . K 10 HOH A 39 339 17 HOH HOH . K 10 HOH A 40 340 98 HOH HOH . K 10 HOH A 41 341 28 HOH HOH . K 10 HOH A 42 342 15 HOH HOH . K 10 HOH A 43 343 44 HOH HOH . K 10 HOH A 44 344 66 HOH HOH . K 10 HOH A 45 345 20 HOH HOH . K 10 HOH A 46 346 51 HOH HOH . K 10 HOH A 47 347 27 HOH HOH . K 10 HOH A 48 348 4 HOH HOH . K 10 HOH A 49 349 46 HOH HOH . K 10 HOH A 50 350 11 HOH HOH . K 10 HOH A 51 351 30 HOH HOH . K 10 HOH A 52 352 52 HOH HOH . K 10 HOH A 53 353 81 HOH HOH . K 10 HOH A 54 354 67 HOH HOH . K 10 HOH A 55 355 16 HOH HOH . K 10 HOH A 56 356 104 HOH HOH . K 10 HOH A 57 357 18 HOH HOH . K 10 HOH A 58 358 58 HOH HOH . K 10 HOH A 59 359 47 HOH HOH . K 10 HOH A 60 360 49 HOH HOH . K 10 HOH A 61 361 54 HOH HOH . K 10 HOH A 62 362 91 HOH HOH . K 10 HOH A 63 363 95 HOH HOH . K 10 HOH A 64 364 77 HOH HOH . K 10 HOH A 65 365 97 HOH HOH . K 10 HOH A 66 366 96 HOH HOH . K 10 HOH A 67 367 93 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 DLY . . . J 9 5.535 9.967 21.844 1 59.68 ? N DLY 209 A 1 HETATM 2 C CA DLY . . . J 9 6.312 9.223 22.863 1 62.74 ? CA DLY 209 A 1 HETATM 3 C C DLY . . . J 9 6.348 10.04 24.13 1 64.98 ? C DLY 209 A 1 HETATM 4 O O DLY . . . J 9 7.383 10.593 24.474 1 64.58 ? O DLY 209 A 1 HETATM 5 C CB DLY . . . J 9 5.748 7.834 23.215 1 65.35 ? CB DLY 209 A 1 HETATM 6 C CG DLY . . . J 9 5.346 7.003 21.992 1 64.61 ? CG DLY 209 A 1 HETATM 7 C CD DLY . . . J 9 5.986 5.615 21.873 1 66.44 ? CD DLY 209 A 1 HETATM 8 C CE DLY . . . J 9 5.815 5.101 20.437 1 65.76 ? CE DLY 209 A 1 HETATM 9 N NZ DLY . . . J 9 5.237 3.769 20.395 1 69.38 ? NZ DLY 209 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 9 #