Research workbench
Insights into the mechanism of deubiquitination by jamm deubiquitinases from co-crystal structures of enzyme with substrate and product
Analyse Insights into the mechanism of deubiquitination by jamm deubiquitinases from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PQT
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amsh-like protease SST2; Protein UBBP4
- EC
- 3.4.19.-
- UniProt
- Q9P371, J3QRK5
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amsh-like protease SST2 (EC 3.4.19.-) | protein | 185 | 26% helix, 35% strand | Q9P371 |
| B | Protein UBBP4 | protein | 76 | 20% helix, 36% strand | J3QRK5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 96 | 0.40 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1247 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4PQT · Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P371 · AlphaFold monomer V2.0 prediction for amsh-like protease SST2 (Q9P371) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9P371
- Every structure of UniProt J3QRK5
- Elsewhere: RCSB PDB 4PQT · PDBe 4PQT · UniProt Q9P371 · UniProt J3QRK5
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