Research workbench
Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor
Analyse Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RE5
- Type
- protein
- Length
- 1,148 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
- Y3A, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 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
- Y3A · N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.77 | 0.82 | 75 | Y3A |
| 2 | 608 | 0.75 | 0.81 | 66 | MPD |
| 3 | 442 | 0.73 | 0.83 | 53 | MPD |
| 4 | 447 | 0.69 | 0.80 | 45 | CL |
| 5 | 426 | 0.68 | 0.80 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1161 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4RE5 · Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor · 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 4RE5 · PDBe 4RE5 · UniProt Q9YBQ2
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