1YVH: C-Cbl TKB Domain

Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide. Determined by X-ray diffraction at 2.05 Å resolution. Released 8 Mar 2005.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,754
Mol. weight: 39.86 kDa
Ligands: MG
Released: 8 Mar 2005

Explore 1YVH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YVH contains 20 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: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	49-51	3
α-helix	53-69	17
α-helix	84-101	18
α-helix	106-111	6
α-helix	113-136	24
α-helix	137-141	5
α-helix	146-168	23
α-helix	170-172	3
α-helix	176-178	3
α-helix	184-194	11
β-strand	199-201	3	1
α-helix	202-212	11
α-helix	218-228	11
β-strand	235-237	3	1
α-helix	238-247	10
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	2
α-helix	274-281	8
α-helix	282-284	3
β-strand	290-295	6	2
β-strand	303-308	6	2
β-strand	314-317	4	2
α-helix	324-333	10
β-strand	339-340	2	2

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	11	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CBL E3 ubiquitin protein ligase	A	protein	329	Homo sapiens	P22681 (AlphaFold model)
13-mer fragment of SH2 and PH domain-containing adapter protein APS	B	protein	13		Q9Z200 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1YVH_1 CBL E3 ubiquitin protein ligase (chains A)
GSLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPP
YILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYE
ENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPW
KSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLA
VTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNK
PLFQALIDGFREGFYLFPDGRNQNPDLTG

Sequence of entity 2 (B), FASTA

>1YVH_2 13-mer fragment of SH2 and PH domain-containing adapter protein APS (chains B)
GRARAVENQYSFY

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Structural Characterization of a Novel Cbl Phosphotyrosine Recognition Motif in the APS Family of Adapter Proteins. Hu, J., Hubbard, S.R. J Biol Chem (2005) 280:18943-18949. DOI 10.1074/jbc.M414157200 · PubMed

Other PDB entries of the same protein (UniProt P22681 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BUX 1.35 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met
3BUW 1.45 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk
7SIY 1.48 Å, cCBL TKB domain in complex with pZAP70 peptide
5HKY 1.8 Å, Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55)…
5HKZ 1.8 Å, Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36-60, pY55) Refined to…
5HKX 1.85 Å, Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution
3PLF 1.92 Å, Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain
2Y1N 2.0 Å, Structure of c-Cbl-ZAP-70 peptide complex
3BUM 2.0 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2
3BUN 2.0 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty4
9ERZ 2.02 Å, Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide
2CBL 2.1 Å, N-terminal domain of cbl in complex with its binding site on zap-70

Browse structure collections

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