MolNFT v1 · #59335 · protein
Crystal structure of C-cbl-tkb domain complexed with its binding motif in syk
3BUW · 13-meric peptide from tyrosine-protein kinase syk: “Crystal structure of C-cbl-tkb domain complexed with its binding motif in syk”. X-ray diffraction, 8 pockets (best druggability 0.76). MolNFT v1 #59335 on GenesisL1: 3D structure…
- PDB
- 3BUW
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 13-meric peptide from tyrosine-protein kinase syk; E3 ubiquitin-protein ligase cbl
- EC
- 6.3.2.-
- UniProt
- P43405, P22681
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 13-meric peptide from tyrosine-protein kinase syk | protein | 9 | 0% helix, 11% strand | P43405 |
| B, D | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 305 | 59% helix, 8% strand | P22681 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.76 | 0.79 | 90 | empty |
| 2 | 97 | 0.53 | 0.84 | 22 | empty |
| 3 | 117 | 0.46 | 0.78 | 18 | empty |
| 4 | 113 | 0.44 | 0.77 | 18 | empty |
| 5 | 83 | 0.34 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 618 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 495 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3BUW · Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk · the same entry in another collection · chain A against A, TM-score 1.00
- P22681 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl (P22681) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P43405 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase syk (P43405) · a predicted model of the same protein · chain A against A, TM-score 0.43
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P43405
- Every structure of UniProt P22681
- Elsewhere: RCSB PDB 3BUW · PDBe 3BUW · UniProt P43405 · UniProt P22681
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