Research workbench
Crystal structure of C-cbl tkb domain in complex with double phosphorylated SPRY2 peptide
Analyse Crystal structure of C-cbl tkb domain in complex with double phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OB1
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12-meric peptide from protein sprouty homolog 2; E3 ubiquitin-protein ligase cbl
- EC
- 6.3.2.-
- UniProt
- O43597, P22681
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 12-meric peptide from protein sprouty homolog 2 | protein | 10 | 0% helix, 0% strand | O43597 |
| B | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 296 | 58% helix, 8% strand | P22681 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.44 | 0.76 | 16 | empty |
| 2 | 80 | 0.42 | 0.79 | 14 | empty |
| 3 | 63 | 0.37 | 0.79 | 16 | empty |
| 4 | 109 | 0.35 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3OB1 · Crystal structure of c-Cbl TKB domain in complex with double phosphorylated Spry2 peptide · 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
- O43597 · AlphaFold monomer V2.0 prediction for protein sprouty homolog 2 (O43597) · a predicted model of the same protein · chain A against A, TM-score 0.44
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 O43597
- Every structure of UniProt P22681
- Elsewhere: RCSB PDB 3OB1 · PDBe 3OB1 · UniProt O43597 · UniProt P22681
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