Research workbench
The UBAP1 subunit of escrt-I interacts with ubiquitin via a novel souba domain
Analyse The UBAP1 subunit of escrt-I interacts with ubiquitin via a novel souba domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AE4
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-associated protein 1
- UniProt
- Q9NZ09
- Ligands
- K, NA
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-associated protein 1 | protein | 114 | 75% helix, 0% strand | Q9NZ09 |
| B | Ubiquitin-associated protein 1 | protein | 115 | 74% helix, 0% strand | Q9NZ09 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.68 | 0.76 | 76 | K, NA |
Interfaces
1 interface between chains.
- A–B · 678 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified, 1 disulfide (engineered, nonstandard, disulfide).
Compared structures
- 4AE4 · The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a novel SOUBA domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZ09 · AlphaFold monomer V2.0 prediction for ubiquitin-associated protein 1 (Q9NZ09) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9NZ09
- Elsewhere: RCSB PDB 4AE4 · PDBe 4AE4 · UniProt Q9NZ09
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.