5HKX: E3 ubiquitin-protein ligase CBL

Name: PDB 5HKX: Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution
Published: 2017-01-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution. Determined by X-ray diffraction at 1.85 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,219
Mol. weight: 45.38 kDa
Ligands: ZN
Released: 18 Jan 2017

Explore 5HKX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HKX contains 24 α-helices and 12 β-strands across 1 chain. 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: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	49-51	3
α-helix	53-70	18
α-helix	73-75	3
α-helix	80	1
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	202-210	9
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	268-271	4	2
α-helix	274-282	9
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
α-helix	350-352	3
α-helix	365-378	14
β-strand	380	1	3
β-strand	388	1	3
α-helix	389	1
β-strand	391-394	4	4
β-strand	399-400	2	4
α-helix	402-410	9
β-strand	425-428	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase CBL	A	protein	392	Homo sapiens	P22681 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5HKX_1 E3 ubiquitin-protein ligase CBL (chains A)
SNAPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYE
GKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLA
ELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMA
LKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQK
FIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGR
NQNPDLTGLCEPTPQDHIKVTQEQYELECEMGSTFQLCKICAENDKDVKIEPCGHLMCTS
CLTSWQESEGQGCPFCRCEIKGTEPIVVDPFD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (NA, EDO) are not listed.

Primary citation

Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution. Zhang, N., Ferris, D., Lovell, S. et al. To be published.

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…
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
1YVH 2.05 Å, Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide
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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