Research workbench
Crystal structure of C-cbl-tkb domain complexed with its binding motif in EGF receptor'
Analyse Crystal structure of C-cbl-tkb domain complexed with its binding motif in EGF… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BUO
- Type
- protein
- Length
- 630 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 13-meric peptide from epidermal growth factor receptor; E3 ubiquitin-protein ligase cbl
- EC
- 6.3.2.-
- UniProt
- P00533, P22681
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 13-meric peptide from epidermal growth factor receptor | protein | 11 | 0% helix, 0% strand | P00533 |
| B, D | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 304 | 56% helix, 8% strand | P22681 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.77 | 0.81 | 68 | empty |
| 2 | 102 | 0.62 | 0.88 | 19 | empty |
| 3 | 88 | 0.62 | 0.89 | 19 | empty |
| 4 | 115 | 0.42 | 0.77 | 20 | empty |
| 5 | 61 | 0.38 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 701 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 616 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3BUO · Crystal structure of c-Cbl-TKB domain complexed with its binding motif in EGF receptor' · the same entry in another collection · chain D against D, 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 0.98
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.32
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 P00533
- Every structure of UniProt P22681
- Elsewhere: RCSB PDB 3BUO · PDBe 3BUO · UniProt P00533 · UniProt P22681
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