3VRP: Tyrosine kinase binding domain of Cbl-c

Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with phospho-EGFR peptide. Determined by X-ray diffraction at 1.52 Å resolution. Released 6 Mar 2013.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,647
Mol. weight: 38.36 kDa
Ligands: CA
Released: 6 Mar 2013

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

Secondary structure: helices and β-sheets

3VRP contains 17 α-helices and 8 β-strands across 2 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: 17 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-31	19
α-helix	40	1
α-helix	44-62	19
α-helix	76-97	22
α-helix	116-138	23
α-helix	140-142	3
α-helix	154-164	11
β-strand	169-171	3	1
α-helix	172-179	8
α-helix	189-198	10
β-strand	205-207	3	1
α-helix	208-217	10
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-233	5
β-strand	238	1	2
α-helix	244-251	8
α-helix	252-254	3
β-strand	260-265	6	2
β-strand	273-278	6	2
β-strand	284-287	4	2
α-helix	294-303	10
β-strand	309-310	2	2
α-helix	315-317	3

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1070	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal transduction protein CBL-C	A	protein	331	Homo sapiens	Q9ULV8 (AlphaFold model)
Epidermal growth factor receptor	B	protein	13	Homo sapiens	P00533 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VRP_1 Signal transduction protein CBL-C (chains A)
GPLGSPEFMALAVAPWGRQWEEARALGRAVRMLQRLEEQCVDPRLSVSPPSLRDLLPRTA
QLLREVAHSRRAAGGGGPGGPGGSGDFLLIYLANLEAKSRQVAALLPPRGRRSANDELFR
AGSRLRRQLAKLAIIFSHMHAELHALFPGGKYCGHMYQLTKAPAHTFWRESCGARCVLPW
AEFESLLGTCHPVEPGCTALALRTTIDLTCSGHVSIFEFDVFTRLFQPWPTLLKNWQLLA
VNHPGYMAFLTYDEVQERLQACRDKPGSYIFRPSCTRLGQWAIGYVSSDGSILQTIPANK
PLSQVLLEGQKDGFYLYPDGKTHNPDLTELG

Sequence of entity 2 (B), FASTA

>3VRP_2 Epidermal growth factor receptor (chains B)
EDSFLQRYSSDPT

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural flexibility regulates phosphopeptide-binding activity of the tyrosine kinase binding domain of Cbl-c. Takeshita, K., Tezuka, T., Isozaki, Y. et al. J Biochem (2012) 152:487-495. DOI 10.1093/jb/mvs085 · PubMed

Other PDB entries of the same protein (UniProt Q9ULV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VRN 1.64 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c
3VRO 1.8 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with…
9OGW 1.8 Å, Identification of ligands for E3 ligases using fragment-based methods
3VRR 2.0 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant) in complex…
3VRQ 2.39 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c (PL mutant)
3OP0 2.52 Å, Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide

Browse structure collections

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