MolNFT v1 · #121090 · protein
Crystal structure of C-cbl tkbd domain in complex with SPRY2 peptide (36-60, PY55) refined to 1.8A resolution (P6 form)
5HKY · E3 ubiquitin-protein ligase cbl: “Crystal structure of C-cbl tkbd domain in complex with SPRY2 peptide (36-60, PY55) refined to 1.8A resolution…”. X-ray diffraction, 2 ligands (NA, CL), 3 pockets (best druggability 0.54). MolNFT v1…
- PDB
- 5HKY
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl; Protein sprouty homolog 2
- EC
- 6.3.2.-
- UniProt
- P22681, O43597
- Ligands
- NA, CL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 303 | 59% helix, 8% strand | P22681 |
| B | Protein sprouty homolog 2 | protein | 22 | 0% helix, 0% strand | O43597 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.54 | 0.81 | 23 | empty |
| 2 | 135 | 0.44 | 0.76 | 25 | empty |
| 3 | 69 | 0.37 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1166 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5HKY · Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55)… · 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 A 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 B against A, TM-score 0.20
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 P22681
- Every structure of UniProt O43597
- Elsewhere: RCSB PDB 5HKY · PDBe 5HKY · UniProt P22681 · UniProt O43597
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