Research workbench
GP78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin
Analyse GP78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LVQ
- Type
- protein
- Length
- 204 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; E3 ubiquitin-protein ligase amfr
- EC
- 6.3.2.-
- UniProt
- P0CG48, Q9UKV5
- Pockets
- 1 · best druggability 0.39
Structure
solution nmr · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin | protein | 76 | 22% helix, 32% strand | P0CG48 |
| D | E3 ubiquitin-protein ligase amfr (EC 6.3.2.-) | protein | 52 | 63% helix, 0% strand | Q9UKV5 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.39 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 711 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 223 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 134 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2LVQ · gp78CUE domain bound to the proximal ubiquitin of K48-linked diubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKV5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase amfr (Q9UKV5) · a predicted model of the same protein · chain D against A, TM-score 0.89
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 P0CG48
- Every structure of UniProt Q9UKV5
- Elsewhere: RCSB PDB 2LVQ · PDBe 2LVQ · UniProt P0CG48 · UniProt Q9UKV5
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