3BUW: C-Cbl-TKB domain

Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk. Determined by X-ray diffraction at 1.45 Å resolution. Released 26 Feb 2008.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,731
Mol. weight: 79.47 kDa
Released: 26 Feb 2008

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

Secondary structure: helices and β-sheets

3BUW 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.

Chains A and C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	324	1	1

Chain B: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	48-51	4
α-helix	53-70	18
α-helix	73-75	3
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	2
α-helix	202-210	9
α-helix	218-228	11
β-strand	235-237	3	2
α-helix	238-247	10
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	1
α-helix	274-281	8
α-helix	282-284	3
β-strand	290-295	6	1
β-strand	303-308	6	1
β-strand	314-317	4	1
α-helix	324-334	11
β-strand	339-340	2	1

Chain D: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3
α-helix	53-70	18
α-helix	73-75	3
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	4
α-helix	202-212	11
α-helix	218-228	11
β-strand	235-237	3	4
α-helix	238-247	10
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	3
α-helix	274-281	8
α-helix	282-284	3
β-strand	290-295	6	3
β-strand	303-308	6	3
β-strand	314-317	4	3
α-helix	324-334	11
β-strand	339-340	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
13-meric peptide from Tyrosine-protein kinase SYK	A, C	protein	13		P43405 (AlphaFold model)
E3 ubiquitin-protein ligase CBL	B, D	protein	329	Homo sapiens	P22681 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3BUW_1 13-meric peptide from Tyrosine-protein kinase SYK (chains A, C)
TVSFNPYEPELAP

Sequence of entity 2 (B, D), FASTA

>3BUW_2 E3 ubiquitin-protein ligase CBL (chains B, D)
GSLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPP
YILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYE
ENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPW
KSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLA
VTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNK
PLFQALIDGFREGFYLFPDGRNQNPDLTG

Primary citation

Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates. Ng, C., Jackson, R.A., Buschdorf, J.P. et al. EMBO J (2008) 27:804-816. DOI 10.1038/emboj.2008.18 · PubMed

Other PDB entries of the same protein (UniProt P43405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YJR 1.32 Å, SYK kinase domain in complex with inhibitor GTC000225
4YJQ 1.34 Å, SYK kinase domain in complex with inhibitor GTC000224
4FYO 1.4 Å, Crystal structure of spleen tyrosine kinase complexed with…
5LMA 1.43 Å, Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine inhibitor
6ZCS 1.47 Å, SYK Kinase domain in complex with azabenzimidazole inhibitor 3
5TIU 1.49 Å, Crystal structure of SYK kinase domain with inhibitor
8XQ1 1.5 Å, Crystal structure of spleen tyrosine kinase(SYK) in complex with SKI-G-1673
8BI2 1.51 Å, Syk kinase domain in complex with macrocyclic inhibitor 20a
4YJT 1.52 Å, The kinase domain of human spleen tyrosine (SYK) in complex with GTC000233
1XBB 1.57 Å, Crystal structure of the syk tyrosine kinase domain with Gleevec
4RX8 1.59 Å, SYK Catalytic Domain Complexed with a Potent Triazine Inhibitor2
4PX6 1.6 Å, SYK catalytic domain in complex with a potent pyridopyrimidinone inhibitor

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