3PFV: Cbl-b TKB domain

Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide. Determined by X-ray diffraction at 2.27 Å resolution. Released 8 Dec 2010.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,435
Mol. weight: 77.58 kDa
Released: 8 Dec 2010

Explore 3PFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PFV contains 40 α-helices and 16 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	45-60	16
α-helix	63-65	3
α-helix	74-91	18
α-helix	95-102	8
α-helix	105-128	24
α-helix	129-133	5
α-helix	138-160	23
α-helix	162-164	3
α-helix	168-170	3
α-helix	171-173	3
α-helix	176-186	11
β-strand	191-193	3	1
α-helix	194-204	11
α-helix	210-220	11
β-strand	227-229	3	1
α-helix	230-239	10
α-helix	243-245	3
α-helix	246-250	5
α-helix	251-255	5
β-strand	260	1	2
α-helix	266-273	8
α-helix	274-276	3
β-strand	282-287	6	2
β-strand	295-300	6	2
β-strand	306-309	4	2
α-helix	316-325	10
β-strand	331-332	2	2
α-helix	342-344	3

Chain B: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	43-60	18
α-helix	63-65	3
α-helix	74-91	18
α-helix	95-102	8
α-helix	105-128	24
α-helix	129-132	4
α-helix	138-160	23
α-helix	162-164	3
α-helix	168-170	3
α-helix	176-186	11
β-strand	191-193	3	3
α-helix	194-204	11
α-helix	210-220	11
β-strand	227-229	3	3
α-helix	230-239	10
α-helix	243-245	3
α-helix	246-250	5
α-helix	251-255	5
β-strand	260	1	4
α-helix	266-274	9
β-strand	282-287	6	4
β-strand	295-300	6	4
β-strand	306-309	4	4
α-helix	316-325	10
β-strand	331-332	2	4
α-helix	342-345	4

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1070	1	2

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1069	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase CBL-B	A, B	protein	315	Homo sapiens	Q13191 (AlphaFold model)
11-meric peptide from Epidermal growth factor receptor	C, D	protein	11	Homo sapiens	P00533 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3PFV_1 E3 ubiquitin-protein ligase CBL-B (chains A, B)
MQAAADRRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYDDNQ
KLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHMLAE
IKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEAMAL
KSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARLQKY
STKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPDGRS
YNPDLTGLAENLYFQ

Sequence of entity 2 (C, D), FASTA

>3PFV_2 11-meric peptide from Epidermal growth factor receptor (chains C, D)
LQRYSSDPTGA

Primary citation

Crystal structure of Cbl-b TKB domain in complex with EGFR pY1069 peptide. Chaikuad, A., Guo, K., Cooper, C.D.O. et al. To be published.

Other PDB entries of the same protein (UniProt Q13191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QTG 1.42 Å, Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 9)
8QTJ 1.52 Å, Crystal structure of Cbl-b in complex with an allosteric inhibitor (compound 30)
2OOA 1.56 Å, crystal structure of the UBA domain from Cbl-b ubiquitin ligase
9FQJ 1.56 Å, E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12)
9XZD 1.65 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 8
9I0B 1.66 Å, E3 ubiquitin ligase CBL-B in complex with inhibitor
2J6F 1.7 Å, N-terminal SH3 domain of cms (CD2AP human homolog) bound to cbl-B peptide
9XZB 1.75 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 2
8VW5 1.76 Å, Crystal structure of Cbl-b TKB bound to compound 2
10ZJ 1.77 Å, Structure of Cbl-B bound to compound 8
9FQH 1.79 Å, E3 ligase Cbl-b in complex with a triazolone core inhibitor (compound 1)
9XZC 1.8 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 6

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