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3buw

Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

13-meric peptide from Tyrosine-protein kinase SYK

OrganismNot specified

UniProt P43405

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 E3 ubiquitin-protein ligase CBL × 1 （P22681） water × 2 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 E3 ubiquitin-protein ligase CBL × 1 （P22681） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1xba 1xbb 1xbc 3buw 3buw 3emg 3fqe 3fqh 3fqh 3fqs 3srv 3srv

98 assemblies; showing the first 12

Homodimer
5t68 8wyw 8xq1 8xq2

4 assemblies

Homotetramer
8xq0

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1a81 1a81 1a81 1a81 1a81 1a81 1a81 1a81 1csy 1csz 3buw 3buw

32 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name KSYK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–13； UniProt 317–329 Author chain C； PDBConstruct 1–13； UniProt 317–329

E3 ubiquitin-protein ligase CBL

Homo sapiens

UniProt P22681

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
2 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 13-meric peptide from Tyrosine-protein kinase SYK × 1 （P43405） water × 2 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 13-meric peptide from Tyrosine-protein kinase SYK × 1 （P43405） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2juj 2k4d 2y1m 2y1m 2y1m 2y1m 2y1m 2y1m 3bum 3bun 3buw 3buw

24 assemblies; showing the first 12

Homodimer
2oo9 2oo9

2 assemblies

Homotetramer

None

Other homooligomers
1b47

1 assemblies

Heteromeric or nucleic-acid complex
1fbv 1yvh 2cbl 2y1n 2y1n 3bum 3bun 3buo 3buo 3buw 3buw 3bux

34 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CBL_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–329； UniProt 23–351 Author chain D； PDBConstruct 1–329； UniProt 23–351

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3buw
Deposition date deposition_date2008-01-03
Structure title titleCrystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk
Keywords keywords;Cbl, TKB, ligase, signal transduction, proto-oncogene, complex, Alternative splicing, ATP-binding, Host-virus interaction, Kinase, Nucleotide-binding, Phosphoprotein, Polymorphism, SH2 domain, Transferase, Tyrosine-protein kinase, Ubl conjugation, Calcium, Cytoplasm, Metal-binding, Ubl conjugation pathway, Zinc, Zinc-finger, LIGASE-SIGNALING PROTEIN COMPLEX ;; LIGASE/SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3buw__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3buw__assembly_1__model_1 | I(q)

10-2 10-1 104 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3buw__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）9.28 Å
Rg (electron density)8.10 Å
Total Rg9.66 Å
Atom count81
Residues8
Excluded volume1398 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3buw__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3buw__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3buw__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3buw__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3buw__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3buw__assembly_6__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3buwb1
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.7 — EF-hand modules in multidomain proteins
Domain ID domain_idd3buwb2
Class classa — All alpha proteins
Fold Fold folda.48 — N-cbl like
Superfamily Superfamily superfamilya.48.1 — N-terminal domain of cbl (N-cbl)
Family Family familya.48.1.1 — N-terminal domain of cbl (N-cbl)
Domain ID domain_idd3buwb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain
Domain ID domain_idd3buwd1
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.7 — EF-hand modules in multidomain proteins
Domain ID domain_idd3buwd2
Class classa — All alpha proteins
Fold Fold folda.48 — N-cbl like
Superfamily Superfamily superfamilya.48.1 — N-terminal domain of cbl (N-cbl)
Family Family familya.48.1.1 — N-terminal domain of cbl (N-cbl)
Domain ID domain_idd3buwd3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain

CATH v4.4 (6 domains)

Domain ID domain_id3buwB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3buwB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3buwB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id3buwD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily20 — Adaptor protein Cbl, N-terminal domain
Domain ID domain_id3buwD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id3buwD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
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7. Citations (1)