data_1KYI # _model_server_result.job_id KxQ8NhzpDPCSJCTJuAEJuw _model_server_result.datetime_utc '2025-02-27 18:47:03' _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 1kyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":175}' # _entry.id 1KYI # _exptl.entry_id 1KYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 722.632 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE' _entity.pdbx_number_of_molecules 12 _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 1KYI _cell.length_a 208.51 _cell.length_b 219.97 _cell.length_c 242.63 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 EA N N ? 4 FA N N ? 4 GA N N ? 4 HA N N ? 4 IA N N ? 4 JA N N ? 4 KA N N ? 4 LA N N ? 4 MA N N ? 4 NA N N ? 4 OA N N ? 4 PA N 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 G OG1 THR 1 G THR 1 1_555 EA CS LVS . G LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 H OG1 THR 1 H THR 1 1_555 FA CS LVS . H LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale3 I OG1 THR 1 I THR 1 1_555 GA CS LVS . I LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.285 ? covale ? covale4 J OG1 THR 1 J THR 1 1_555 HA CS LVS . J LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale5 K OG1 THR 1 K THR 1 1_555 IA CS LVS . K LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale6 L OG1 THR 1 L THR 1 1_555 JA CS LVS . L LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale7 M OG1 THR 1 M THR 1 1_555 KA CS LVS . M LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale8 N OG1 THR 1 N THR 1 1_555 LA CS LVS . N LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 O OG1 THR 1 O THR 1 1_555 MA CS LVS . O LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 P OG1 THR 1 P THR 1 1_555 NA CS LVS . P LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale11 Q OG1 THR 1 Q THR 1 1_555 OA CS LVS . Q LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale12 R OG1 THR 1 R THR 1 1_555 PA CS LVS . R LVS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _chem_comp.formula 'C28 H43 I N4 O8 S' _chem_comp.formula_weight 722.632 _chem_comp.id LVS _chem_comp.mon_nstd_flag . _chem_comp.name '4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE' _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 CB1 CG1 LVS sing 241 n n CB1 CA1 LVS sing 242 n n CB1 HB11 LVS sing 243 n n CB1 HB12 LVS sing 244 n n CG1 CD1 LVS sing 245 n n CG1 CD2 LVS sing 246 n n CG1 HG1 LVS sing 247 n n CD1 HD11 LVS sing 248 n n CD1 HD12 LVS sing 249 n n CD1 HD13 LVS sing 250 n n CD2 HD21 LVS sing 251 n n CD2 HD22 LVS sing 252 n n CD2 HD23 LVS sing 253 n n C1 O1 LVS doub 254 n n C1 CA1 LVS sing 255 n n C1 N2 LVS sing 256 n n N1 CA1 LVS sing 257 n n N1 C3 LVS sing 258 n n N1 HN1 LVS sing 259 n n CA1 HA1 LVS sing 260 n n N2 CA2 LVS sing 261 n n N2 HN2 LVS sing 262 n n CA2 CB2 LVS sing 263 n n CA2 C2 LVS sing 264 n n CA2 HA2 LVS sing 265 n n CB2 CG2 LVS sing 266 n n CB2 HB21 LVS sing 267 n n CB2 HB22 LVS sing 268 n n CG2 CD3 LVS sing 269 n n CG2 CD4 LVS sing 270 n n CG2 HG2 LVS sing 271 n n CD3 HD31 LVS sing 272 n n CD3 HD32 LVS sing 273 n n CD3 HD33 LVS sing 274 n n CD4 HD41 LVS sing 275 n n CD4 HD42 LVS sing 276 n n CD4 HD43 LVS sing 277 n n C2 O2 LVS doub 278 n n C2 N3 LVS sing 279 n n N3 CA3 LVS sing 280 n n N3 HN3 LVS sing 281 n n CA3 CS LVS sing 282 n n CA3 CB3 LVS sing 283 n n CA3 HA3 LVS sing 284 n n CS C2' LVS doub 285 n n CS HCS LVS sing 286 n n CB3 CG3 LVS sing 287 n n CB3 HB31 LVS sing 288 n n CB3 HB32 LVS sing 289 n n CG3 CD5 LVS sing 290 n n CG3 CD6 LVS sing 291 n n CG3 HG3 LVS sing 292 n n CD5 HD51 LVS sing 293 n n CD5 HD52 LVS sing 294 n n CD5 HD53 LVS sing 295 n n CD6 HD61 LVS sing 296 n n CD6 HD62 LVS sing 297 n n CD6 HD63 LVS sing 298 n n C1' S LVS sing 299 n n C1' "H1'1" LVS sing 300 n n C1' "H1'2" LVS sing 301 n n C1' "H1'3" LVS sing 302 n n S O1' LVS doub 303 n n S O2' LVS doub 304 n n S C2' LVS sing 305 n n C2' H2' LVS sing 306 n n C3 C4 LVS sing 307 n n C3 O6 LVS doub 308 n n C4 C5 LVS sing 309 n n C4 HC41 LVS sing 310 n n C4 HC42 LVS sing 311 n n C5 C6 LVS doub 312 n y C5 C10 LVS sing 313 n y C6 C7 LVS sing 314 n y C6 HC6 LVS sing 315 n n C7 C8 LVS doub 316 n y C7 N4 LVS sing 317 n n C8 C9 LVS sing 318 n y C8 O5 LVS sing 319 n n C9 C10 LVS doub 320 n y C9 I LVS sing 321 n n C10 H10 LVS sing 322 n n N4 O3 LVS doub 323 n n N4 O4 LVS sing 324 n n O5 HO5 LVS sing 325 n n # _atom_sites.entry_id 1KYI _atom_sites.fract_transf_matrix[1][1] 0.004796 _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] 0.004546 _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] 0.004122 _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 Y 3 ATP A 1 450 450 ATP ATP . Z 3 ATP B 1 451 450 ATP ATP . AA 3 ATP C 1 452 450 ATP ATP . BA 3 ATP D 1 453 450 ATP ATP . CA 3 ATP E 1 454 450 ATP ATP . DA 3 ATP F 1 455 450 ATP ATP . EA 4 LVS G 1 175 174 LVS LEU . FA 4 LVS H 1 175 174 LVS LEU . GA 4 LVS I 1 175 174 LVS LEU . HA 4 LVS J 1 175 174 LVS LEU . IA 4 LVS K 1 175 174 LVS LEU . JA 4 LVS L 1 175 174 LVS LEU . KA 4 LVS M 1 175 174 LVS LEU . LA 4 LVS N 1 175 174 LVS LEU . MA 4 LVS O 1 175 174 LVS LEU . NA 4 LVS P 1 175 174 LVS LEU . OA 4 LVS Q 1 175 174 LVS LEU . PA 4 LVS R 1 175 174 LVS LEU . QA 3 ATP S 1 456 450 ATP ATP . RA 3 ATP T 1 457 450 ATP ATP . SA 3 ATP U 1 458 450 ATP ATP . TA 3 ATP V 1 459 450 ATP ATP . UA 3 ATP W 1 460 450 ATP ATP . VA 3 ATP X 1 461 450 ATP ATP . # 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 CB1 LVS . . . HA 4 141.173 56.45 77.335 1 32.61 ? CB1 LVS 175 J 1 HETATM 2 C CG1 LVS . . . HA 4 140.825 54.965 77.184 1 30.31 ? CG1 LVS 175 J 1 HETATM 3 C CD1 LVS . . . HA 4 141.998 54.277 76.525 1 33.2 ? CD1 LVS 175 J 1 HETATM 4 C CD2 LVS . . . HA 4 140.551 54.303 78.536 1 27.34 ? CD2 LVS 175 J 1 HETATM 5 C C1 LVS . . . HA 4 140.529 58.325 75.842 1 34.49 ? C1 LVS 175 J 1 HETATM 6 O O1 LVS . . . HA 4 140.508 59.288 76.608 1 32.02 ? O1 LVS 175 J 1 HETATM 7 N N1 LVS . . . HA 4 142.937 57.801 76.108 1 47.16 ? N1 LVS 175 J 1 HETATM 8 C CA1 LVS . . . HA 4 141.538 57.208 76.04 1 39.01 ? CA1 LVS 175 J 1 HETATM 9 N N2 LVS . . . HA 4 139.684 58.234 74.831 1 43.78 ? N2 LVS 175 J 1 HETATM 10 C CA2 LVS . . . HA 4 138.75 59.329 74.65 1 39.66 ? CA2 LVS 175 J 1 HETATM 11 C CB2 LVS . . . HA 4 139.215 60.303 73.579 1 30.3 ? CB2 LVS 175 J 1 HETATM 12 C CG2 LVS . . . HA 4 140.61 60.889 73.781 1 27.44 ? CG2 LVS 175 J 1 HETATM 13 C CD3 LVS . . . HA 4 141.628 59.822 73.279 1 27.62 ? CD3 LVS 175 J 1 HETATM 14 C CD4 LVS . . . HA 4 140.775 62.208 72.989 1 21.34 ? CD4 LVS 175 J 1 HETATM 15 C C2 LVS . . . HA 4 137.394 58.869 74.278 1 39.46 ? C2 LVS 175 J 1 HETATM 16 O O2 LVS . . . HA 4 137.141 57.657 74.213 1 42.28 ? O2 LVS 175 J 1 HETATM 17 N N3 LVS . . . HA 4 136.518 59.841 74.032 1 39.65 ? N3 LVS 175 J 1 HETATM 18 C CA3 LVS . . . HA 4 135.159 59.542 73.647 1 40.52 ? CA3 LVS 175 J 1 HETATM 19 C CS LVS . . . HA 4 134.279 60.631 73.17 1 41.46 ? CS LVS 175 J 1 HETATM 20 C CB3 LVS . . . HA 4 134.464 58.78 74.799 1 39.53 ? CB3 LVS 175 J 1 HETATM 21 C CG3 LVS . . . HA 4 134.615 59.149 76.292 1 37.27 ? CG3 LVS 175 J 1 HETATM 22 C CD5 LVS . . . HA 4 133.934 60.463 76.657 1 37.09 ? CD5 LVS 175 J 1 HETATM 23 C CD6 LVS . . . HA 4 134.033 58.047 77.132 1 35.93 ? CD6 LVS 175 J 1 HETATM 24 C C1' LVS . . . HA 4 135.008 63.852 71.067 1 42.84 ? C1' LVS 175 J 1 HETATM 25 S S LVS . . . HA 4 136.018 62.513 71.78 1 42.75 ? S LVS 175 J 1 HETATM 26 O O1' LVS . . . HA 4 136.317 61.375 70.882 1 40.18 ? O1' LVS 175 J 1 HETATM 27 O O2' LVS . . . HA 4 137.298 63.011 72.314 1 41.83 ? O2' LVS 175 J 1 HETATM 28 C C2' LVS . . . HA 4 134.973 61.97 73.185 1 42.57 ? C2' LVS 175 J 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #