Research workbench
Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1
Analyse Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VE6
- Type
- protein
- Length
- 1,148 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Aeropyrum pernix
- Molecule
- Acylamino-acid-releasing enzyme
- EC
- 3.4.19.1
- UniProt
- Q9YBQ2
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 574 | 22% helix, 41% strand | Q9YBQ2 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.77 | 0.83 | 80 | GOL |
| 2 | 586 | 0.74 | 0.81 | 80 | empty |
| 3 | 279 | 0.70 | 0.85 | 38 | GOL |
| 4 | 333 | 0.69 | 0.82 | 44 | empty |
| 5 | 453 | 0.69 | 0.80 | 57 | BOG |
Interfaces
1 interface between chains.
- A–B · 1356 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1VE6 · Crystal structure of an acylpeptide HYDROLASE/ESTERASE from aeropyrum pernix K1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YBQ2 · AlphaFold monomer V2.0 prediction for acylamino-acid-releasing enzyme (Q9YBQ2) · a predicted model of the same protein · chain B 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 Q9YBQ2
- Elsewhere: RCSB PDB 1VE6 · PDBe 1VE6 · UniProt Q9YBQ2
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