1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Huang, A. De Jong, R.N. Wienk, H. Winkler, S.G. Timmers, H.T.M. Boelens, R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer UK J.Mol.Biol. JMOBAK 0070 0022-2836 385 507 519 10.1016/j.jmb.2008.10.044 18996392 E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity 2009 10.2210/pdb2k4d/pdb pdb_00002k4d 9387.662 E3 ubiquitin-protein ligase CBL 6.3.2.- RING domain, residues 358-437 1 man polymer 65.409 ZINC ION 2 syn non-polymer Signal transduction protein CBL, Proto-oncogene c-CBL, Casitas B-lineage lymphoma proto-oncogene, RING finger protein 55 no no GSLQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF DPR GSLQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF DPR A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human Homo Escherichia sample CBL, CBL2, RNF55 9606 Homo sapiens 562 Escherichia coli BL21(DE3) Rosetta 2 pLICHISGST vector pdbx_database_status pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif database_2 pdbx_database_status struct_ref struct_site repository Initial release Version format compliance Data collection Database references Derived calculations Other Database references Derived calculations Other 1 0 2009-01-20 1 1 2011-07-13 1 2 2020-02-26 1 3 2023-06-14 _pdbx_database_status.status_code_cs _pdbx_nmr_spectrometer.model _struct_ref_seq_dif.details _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _struct_ref.pdbx_seq_one_letter_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id c-Cbl UbcH7 crystal structure BMRB Y PDBJ 2008-06-06 REL REL REL REL ZN ZINC ION target function 100 20 1 2D 1H-15N HSQC 2D 1H-13C HSQC 2D 1H-1H NOESY 3D CBCA(CO)NH 3D C(CO)NH 3D HNCO 3D HNCA 3D HNCACB 3D HBHA(CO)NH 3D HN(CO)CA 3D HCCH-TOCSY 3D 1H-15N NOESY 3D 1H-15N TOCSY 3D 1H-13C NOESY 3D HNCACO 3D CNH-NOESY 1 mM [U-99% 15N] 50 mM 100 mM 100 uM 0.2 mM 5 mM 1 mM [U-99% 13C; U-99% 15N] 50 mM 100 mM 100 uM 0.2 mM 5 mM 150 7.3 ambient 298 K RECOORD approach simulated annealing 1 lowest energy 1mM [U-99% 15N] c-Cbl; 50mM potassium phosphate; 100mM sodium chloride; 0.100mM zinc chloride; 0.2mM PMSF; 5mM DTT; 95% H2O/5% D2O 95% H2O/5% D2O 1mM [U-99% 13C; U-99% 15N] c-Cbl; 50mM potassium phosphate; 100mM sodium chloride; 0.100mM zinc chloride; 0.2mM PMSF; 5mM DTT; 95% H2O/5% D2O 95% H2O/5% D2O Guntert, Mumenthaler and Wuthrich structure solution CYANA 2.1.1 Guntert, Mumenthaler and Wuthrich refinement CYANA 2.1.1 600 Bruker AVANCE Bruker Avance 700 Bruker AVANCE Bruker Avance ZN 500 2 ZN ZN 500 A ZN 600 2 ZN ZN 600 A GLY 355 n 1 GLY 355 A SER 356 n 2 SER 356 A LEU 357 n 3 LEU 357 A GLN 358 n 4 GLN 358 A ASP 359 n 5 ASP 359 A HIS 360 n 6 HIS 360 A ILE 361 n 7 ILE 361 A LYS 362 n 8 LYS 362 A VAL 363 n 9 VAL 363 A THR 364 n 10 THR 364 A GLN 365 n 11 GLN 365 A GLU 366 n 12 GLU 366 A GLN 367 n 13 GLN 367 A TYR 368 n 14 TYR 368 A GLU 369 n 15 GLU 369 A LEU 370 n 16 LEU 370 A TYR 371 n 17 TYR 371 A CYS 372 n 18 CYS 372 A GLU 373 n 19 GLU 373 A MET 374 n 20 MET 374 A GLY 375 n 21 GLY 375 A SER 376 n 22 SER 376 A THR 377 n 23 THR 377 A PHE 378 n 24 PHE 378 A GLN 379 n 25 GLN 379 A LEU 380 n 26 LEU 380 A CYS 381 n 27 CYS 381 A LYS 382 n 28 LYS 382 A ILE 383 n 29 ILE 383 A CYS 384 n 30 CYS 384 A ALA 385 n 31 ALA 385 A GLU 386 n 32 GLU 386 A ASN 387 n 33 ASN 387 A ASP 388 n 34 ASP 388 A LYS 389 n 35 LYS 389 A ASP 390 n 36 ASP 390 A VAL 391 n 37 VAL 391 A LYS 392 n 38 LYS 392 A ILE 393 n 39 ILE 393 A GLU 394 n 40 GLU 394 A PRO 395 n 41 PRO 395 A CYS 396 n 42 CYS 396 A GLY 397 n 43 GLY 397 A HIS 398 n 44 HIS 398 A LEU 399 n 45 LEU 399 A MET 400 n 46 MET 400 A CYS 401 n 47 CYS 401 A THR 402 n 48 THR 402 A SER 403 n 49 SER 403 A CYS 404 n 50 CYS 404 A LEU 405 n 51 LEU 405 A THR 406 n 52 THR 406 A SER 407 n 53 SER 407 A TRP 408 n 54 TRP 408 A GLN 409 n 55 GLN 409 A GLU 410 n 56 GLU 410 A SER 411 n 57 SER 411 A GLU 412 n 58 GLU 412 A GLY 413 n 59 GLY 413 A GLN 414 n 60 GLN 414 A GLY 415 n 61 GLY 415 A CYS 416 n 62 CYS 416 A PRO 417 n 63 PRO 417 A PHE 418 n 64 PHE 418 A CYS 419 n 65 CYS 419 A ARG 420 n 66 ARG 420 A CYS 421 n 67 CYS 421 A GLU 422 n 68 GLU 422 A ILE 423 n 69 ILE 423 A LYS 424 n 70 LYS 424 A GLY 425 n 71 GLY 425 A THR 426 n 72 THR 426 A GLU 427 n 73 GLU 427 A PRO 428 n 74 PRO 428 A ILE 429 n 75 ILE 429 A VAL 430 n 76 VAL 430 A VAL 431 n 77 VAL 431 A ASP 432 n 78 ASP 432 A PRO 433 n 79 PRO 433 A PHE 434 n 80 PHE 434 A ASP 435 n 81 ASP 435 A PRO 436 n 82 PRO 436 A ARG 437 n 83 ARG 437 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 A O MET 400 A O MET 46 A N VAL 391 A N VAL 37 A N LYS 392 A N LYS 38 A O GLU 427 A O GLU 73 1 A A HZ3 OE2 LYS GLU 392 394 1.59 2 A A HZ1 OE2 LYS GLU 392 394 1.57 3 A A HZ2 OE2 LYS GLU 392 394 1.57 12 A A OD1 HZ3 ASP LYS 388 389 1.56 17 A A HZ2 OE1 LYS GLU 392 394 1.57 20 A A HZ2 OE2 LYS GLU 392 394 1.60 13 A ARG 420 0.080 SIDE CHAIN 1 A GLU 366 175.34 134.34 1 A LEU 370 -76.19 30.66 1 A MET 374 62.08 84.06 1 A LEU 380 89.79 142.71 1 A ALA 385 71.66 -7.94 1 A MET 400 -173.04 -176.86 1 A GLU 412 74.84 107.03 1 A GLN 414 -78.11 49.18 1 A PHE 418 -80.29 -73.35 1 A GLU 422 -36.99 116.43 1 A ILE 429 -108.54 -86.99 1 A VAL 430 72.46 87.73 1 A PHE 434 64.69 -78.83 1 A ASP 435 -154.36 89.19 2 A GLN 358 66.42 178.88 2 A ASP 359 -123.31 -78.40 2 A HIS 360 66.57 -53.37 2 A THR 364 -103.50 -100.37 2 A CYS 372 81.12 107.52 2 A GLU 386 -126.20 -54.00 2 A GLU 412 63.04 78.28 2 A PHE 418 -90.67 -67.67 2 A GLU 422 -44.55 109.68 3 A LYS 362 66.27 -177.96 3 A VAL 363 -100.73 74.94 3 A MET 374 72.31 -52.24 3 A GLU 412 66.31 89.44 3 A ARG 420 57.95 72.37 3 A CYS 421 -126.56 -158.91 3 A LYS 424 -123.65 -57.40 3 A ILE 429 61.07 149.68 3 A ASP 435 52.10 71.46 4 A SER 356 -102.51 -74.96 4 A GLN 358 60.97 -175.12 4 A ASP 359 -94.66 -70.51 4 A GLU 412 74.50 89.21 4 A PHE 418 -93.38 -72.44 4 A GLU 422 -38.34 115.53 4 A LYS 424 -134.99 -39.80 4 A PRO 433 -61.62 92.04 5 A ASP 359 59.60 80.04 5 A GLN 367 -72.57 31.24 5 A MET 374 -177.31 91.72 5 A ALA 385 70.87 -37.00 5 A GLU 412 72.72 92.93 5 A PHE 418 -91.91 -72.45 5 A GLU 422 -35.73 124.30 5 A PHE 434 -92.14 -63.21 6 A SER 356 63.66 95.76 6 A ILE 361 75.34 126.98 6 A GLU 366 -153.21 -48.96 6 A CYS 372 -56.07 108.72 6 A GLU 386 -122.91 -55.93 6 A MET 400 176.94 -168.93 6 A GLU 412 63.79 79.76 6 A GLU 422 -39.01 129.05 6 A PRO 433 -66.72 88.40 7 A ILE 361 -154.96 -48.48 7 A CYS 372 68.62 115.58 7 A MET 400 -177.93 -173.23 7 A GLU 412 65.29 94.22 7 A VAL 430 -106.46 41.90 8 A ASP 359 59.54 -158.94 8 A HIS 360 59.53 -164.23 8 A GLU 366 58.44 71.89 8 A LEU 370 -68.26 2.13 8 A MET 374 61.34 -175.40 8 A MET 400 -170.46 -174.96 8 A GLU 412 68.25 104.05 8 A PHE 418 -77.47 -70.74 8 A ILE 429 -102.10 -66.98 8 A VAL 430 71.04 86.03 8 A PRO 436 -90.20 34.59 9 A THR 364 -64.40 -98.26 9 A GLU 412 70.99 94.79 9 A PHE 418 -81.99 -79.02 9 A PRO 433 -74.16 35.30 10 A GLN 358 -174.13 86.84 10 A LYS 362 -137.36 -68.81 10 A GLU 366 71.59 122.13 10 A LEU 370 -64.38 6.61 10 A CYS 372 -70.77 -75.87 10 A GLU 373 -155.96 13.77 10 A MET 374 55.74 -148.96 10 A THR 377 -66.67 97.27 10 A PHE 378 -132.93 -38.85 10 A GLU 386 -126.24 -55.82 10 A MET 400 -170.71 -175.01 10 A GLU 412 83.51 87.44 10 A PHE 418 -92.24 -71.28 10 A GLU 422 -33.91 118.32 11 A SER 356 62.53 173.59 11 A HIS 360 -128.96 -78.11 11 A THR 364 -125.28 -55.36 11 A GLU 369 -47.96 -15.97 11 A GLU 386 -122.24 -50.57 11 A GLU 412 164.57 -72.77 11 A PHE 418 -83.80 -76.65 11 A GLU 422 -27.65 120.16 11 A PHE 434 66.48 -68.60 11 A ASP 435 -155.15 89.96 12 A HIS 360 -122.70 -79.35 12 A ILE 361 60.31 95.27 12 A LYS 362 68.23 -177.68 12 A GLN 367 -66.51 32.05 12 A MET 374 -134.43 -65.57 12 A GLU 386 -138.28 -50.99 12 A GLU 412 179.31 -75.14 12 A GLU 422 -34.14 113.77 13 A GLN 358 73.66 -77.31 13 A ASP 359 61.01 -69.98 13 A GLU 366 58.65 89.18 13 A MET 374 67.35 165.67 13 A GLU 412 81.54 87.33 13 A GLU 422 1.26 105.58 13 A PRO 433 -69.68 59.03 14 A THR 364 -144.01 -59.94 14 A CYS 372 59.23 -86.96 14 A MET 374 73.04 -56.29 14 A GLN 379 69.22 -71.97 14 A GLU 412 69.44 100.56 14 A ARG 420 53.56 70.10 14 A GLU 422 -28.27 115.35 14 A PHE 434 62.07 -77.03 15 A PHE 378 -154.57 -32.02 15 A GLN 379 -87.10 36.35 15 A GLU 412 71.58 98.83 15 A PHE 418 -80.13 -71.95 15 A GLU 422 -26.68 131.41 15 A ILE 429 -80.09 -75.32 15 A VAL 430 70.73 94.66 15 A ASP 435 -154.59 85.19 16 A ASP 359 82.22 -4.42 16 A LYS 362 178.21 151.14 16 A CYS 372 52.26 78.27 16 A GLU 412 76.65 97.96 16 A GLU 422 -32.58 119.99 16 A LYS 424 -134.92 -41.89 16 A PRO 433 -83.37 39.58 16 A PRO 436 -94.92 32.15 17 A ASP 359 -155.45 -71.16 17 A LYS 362 71.34 167.06 17 A THR 364 40.15 -97.36 17 A GLU 373 76.33 103.53 17 A GLU 412 75.93 94.36 17 A ARG 420 67.20 69.96 17 A GLU 422 -19.16 110.07 17 A PRO 433 -65.61 80.77 17 A PRO 436 -89.24 43.27 18 A THR 364 -120.42 -58.90 18 A CYS 372 -168.05 -45.74 18 A GLN 379 137.98 -38.27 18 A MET 400 -172.62 -174.84 18 A GLU 412 79.50 98.19 18 A ARG 420 62.11 76.66 18 A GLU 422 -22.72 109.15 18 A PHE 434 64.50 -69.75 18 A PRO 436 -101.88 -165.92 19 A GLN 358 -168.48 -46.52 19 A HIS 360 68.13 83.30 19 A GLU 366 -144.64 -6.67 19 A CYS 372 -127.92 -69.41 19 A GLN 379 -79.65 -164.92 19 A LEU 380 59.38 109.93 19 A ALA 385 70.70 -28.91 19 A GLU 412 66.55 98.16 19 A ASP 435 -153.32 89.11 20 A ASP 359 -138.95 -42.46 20 A ILE 361 62.42 158.50 20 A THR 364 -134.25 -40.53 20 A ALA 385 71.50 -3.64 20 A GLU 412 68.67 95.42 20 A ASP 435 58.81 80.96 E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity 1 N N 2 N N 2 N N A CYS 401 A CYS 47 HELX_P A GLU 410 A GLU 56 1 1 10 disulf 2.950 A CYS 401 A SG CYS 47 1_555 A CYS 404 A SG CYS 50 1_555 metalc 1.913 A CYS 381 A SG CYS 27 1_555 A ZN 500 B ZN ZN 1_555 LIGASE protein, ubiquitin, c-Cbl, UbcH5B, UbcH7, Calcium, Cytoplasm, Ligase, Metal-binding, Phosphoprotein, Proto-oncogene, SH2 domain, Ubl conjugation pathway, Zinc, Zinc-finger A GLU 394 A GLU 40 1 A PRO 395 A PRO 41 0.44 A GLU 394 A GLU 40 2 A PRO 395 A PRO 41 -1.57 A GLU 394 A GLU 40 3 A PRO 395 A PRO 41 0.29 A GLU 394 A GLU 40 4 A PRO 395 A PRO 41 -0.05 A GLU 394 A GLU 40 5 A PRO 395 A PRO 41 1.72 A GLU 394 A GLU 40 6 A PRO 395 A PRO 41 -0.20 A GLU 394 A GLU 40 7 A PRO 395 A PRO 41 2.15 A GLU 394 A GLU 40 8 A PRO 395 A PRO 41 0.96 A GLU 394 A GLU 40 9 A PRO 395 A PRO 41 -2.28 A GLU 394 A GLU 40 10 A PRO 395 A PRO 41 -0.66 A GLU 394 A GLU 40 11 A PRO 395 A PRO 41 -2.47 A GLU 394 A GLU 40 12 A PRO 395 A PRO 41 -1.33 A GLU 394 A GLU 40 13 A PRO 395 A PRO 41 1.99 A GLU 394 A GLU 40 14 A PRO 395 A PRO 41 -1.60 A GLU 394 A GLU 40 15 A PRO 395 A PRO 41 1.26 A GLU 394 A GLU 40 16 A PRO 395 A PRO 41 0.64 A GLU 394 A GLU 40 17 A PRO 395 A PRO 41 -1.40 A GLU 394 A GLU 40 18 A PRO 395 A PRO 41 1.95 A GLU 394 A GLU 40 19 A PRO 395 A PRO 41 -0.96 A GLU 394 A GLU 40 20 A PRO 395 A PRO 41 0.98 CBL_HUMAN UNP 1 358 P22681 QDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPFDPR 358 437 2K4D 358 437 P22681 A 1 4 83 1 expression tag GLY 355 2K4D A P22681 UNP 1 1 expression tag SER 356 2K4D A P22681 UNP 2 1 expression tag LEU 357 2K4D A P22681 UNP 3 3 anti-parallel anti-parallel A HIS 398 A HIS 44 A MET 400 A MET 46 A VAL 391 A VAL 37 A PRO 395 A PRO 41 A ILE 423 A ILE 69 A PRO 428 A PRO 74 BINDING SITE FOR RESIDUE ZN A 500 A ZN 500 Software 5 BINDING SITE FOR RESIDUE ZN A 600 A ZN 600 Software 4 A CYS 381 A CYS 27 5 1_555 A ILE 383 A ILE 29 5 1_555 A CYS 384 A CYS 30 5 1_555 A ASN 387 A ASN 33 5 1_555 A ASP 388 A ASP 34 5 1_555 A ILE 393 A ILE 39 4 1_555 A CYS 396 A CYS 42 4 1_555 A HIS 398 A HIS 44 4 1_555 A CYS 421 A CYS 67 4 1_555