Research workbench
Crystal structure of an acylpeptide HYDROLASE/ESTERASE from aeropyrum pernix K1 in complex with P-nitrophenyl phosphate
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
- 1VE7
- Type
- protein
- Length
- 1,146 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylamino-acid-releasing enzyme
- EC
- 3.4.19.1
- UniProt
- Q9YBQ2
- Ligands
- 4NP
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 573 | 21% helix, 41% strand | Q9YBQ2 |
Ligands and binding sites
- 4NP · 4-nitrophenyl phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.80 | 0.82 | 110 | 4NP |
| 2 | 687 | 0.77 | 0.82 | 81 | GOL |
| 3 | 605 | 0.77 | 0.83 | 73 | 4NP |
| 4 | 407 | 0.69 | 0.81 | 48 | empty |
| 5 | 205 | 0.51 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1192 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1VE7 · Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1 in… · the same entry in another collection · chain B against B, 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 1VE7 · PDBe 1VE7 · UniProt Q9YBQ2
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