MolNFT v1 · #146654 · protein
KLHDC2 ubiquitin ligase in complex with selk C-end degron
6DO3 · Kelch domain-containing protein 2: “KLHDC2 ubiquitin ligase in complex with selk C-end degron”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #146654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DO3
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch domain-containing protein 2; Selk C-end degron
- UniProt
- Q9Y2U9
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kelch domain-containing protein 2 | protein | 317 | 2% helix, 52% strand | Q9Y2U9 |
| C, D | Selk C-end degron | protein | 7 | 43% helix, 0% strand | — |
| B | Kelch domain-containing protein 2 | protein | 317 | 2% helix, 49% strand | Q9Y2U9 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.79 | 0.85 | 41 | empty |
| 2 | 552 | 0.78 | 0.85 | 40 | empty |
| 3 | 830 | 0.73 | 0.78 | 65 | empty |
| 4 | 52 | 0.34 | 0.79 | 11 | empty |
| 5 | 75 | 0.30 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–D · 457 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 338 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6DO3 · KLHDC2 ubiquitin ligase in complex with SelK C-end degron · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2U9 · AlphaFold monomer V2.0 prediction for kelch domain-containing protein 2 (Q9Y2U9) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9Y2U9
- Elsewhere: RCSB PDB 6DO3 · PDBe 6DO3 · UniProt Q9Y2U9
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