Research workbench
KLHDC2 ubiquitin ligase in complex with USP1 C-end degron
Analyse KLHDC2 ubiquitin ligase in complex with USP1 C-end degron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DO5
- Type
- protein
- Length
- 647 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch domain-containing protein 2; USP1 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, 49% strand | Q9Y2U9 |
| B | Kelch domain-containing protein 2 | protein | 316 | 2% helix, 50% strand | Q9Y2U9 |
| D, C | USP1 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 | 548 | 0.79 | 0.85 | 43 | empty |
| 2 | 528 | 0.78 | 0.85 | 44 | empty |
| 3 | 707 | 0.72 | 0.79 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–D · 430 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 427 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6DO5 · KLHDC2 ubiquitin ligase in complex with USP1 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 6DO5 · PDBe 6DO5 · UniProt Q9Y2U9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.