MolNFT v1 · #121089 · protein
Crystal structure of C-cbl tkbd-ring domains (Y371E mutant) refined to 1.85 a resolution
5HKX · E3 ubiquitin-protein ligase cbl: “Crystal structure of C-cbl tkbd-ring domains (Y371E mutant) refined to 1.85 a resolution”. X-ray diffraction, 2 ligands (ZN, NA), 3 pockets (best druggability 0.78). MolNFT v1 #121089 on GenesisL1…
- PDB
- 5HKX
- Type
- protein
- Length
- 374 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase cbl
- EC
- 6.3.2.-
- UniProt
- P22681
- Ligands
- ZN, NA
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 374 | 54% helix, 11% strand | P22681 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · 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 | 927 | 0.78 | 0.80 | 82 | empty |
| 2 | 70 | 0.40 | 0.80 | 15 | empty |
| 3 | 88 | 0.32 | 0.73 | 18 | empty |
Compared structures
- 5HKX · Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution · 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 0.82
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
- Elsewhere: RCSB PDB 5HKX · PDBe 5HKX · UniProt P22681
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