MolNFT v1 · #146655 · protein
KLHDC2 ubiquitin ligase in complex with sels C-end degron
6DO4 · Kelch domain-containing protein 2: “KLHDC2 ubiquitin ligase in complex with sels C-end degron”. X-ray diffraction, 3 pockets (best druggability 0.79). MolNFT v1 #146655 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DO4
- Type
- protein
- Length
- 649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch domain-containing protein 2; Sels C-end degron
- UniProt
- Q9Y2U9
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kelch domain-containing protein 2 | protein | 319 | 2% helix, 51% strand | Q9Y2U9 |
| B | Kelch domain-containing protein 2 | protein | 318 | 2% helix, 47% strand | Q9Y2U9 |
| D, C | Sels C-end degron | protein | 6 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.79 | 0.85 | 43 | empty |
| 2 | 534 | 0.79 | 0.86 | 42 | empty |
| 3 | 719 | 0.73 | 0.79 | 65 | empty |
Interfaces
3 interfaces between chains.
- B–D · 389 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 384 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6DO4 · KLHDC2 ubiquitin ligase in complex with SelS 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 A 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 6DO4 · PDBe 6DO4 · UniProt Q9Y2U9
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