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
- 4RE6
- Type
- protein
- Length
- 2,305 residues
- Chains
- 4
- 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
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 577 | 22% helix, 41% strand | Q9YBQ2 |
| B | Acylamino-acid-releasing enzyme (EC 3.4.19.1) | protein | 574 | 21% helix, 40% 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, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.80 | 0.81 | 119 | Y3A |
| 2 | 563 | 0.75 | 0.82 | 70 | Y3A, CL |
| 3 | 981 | 0.74 | 0.77 | 113 | empty |
| 4 | 212 | 0.74 | 0.89 | 28 | empty |
| 5 | 217 | 0.71 | 0.87 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1358 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1351 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 4RE6 · Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- Q9YBQ2 · AlphaFold monomer V2.0 prediction for acylamino-acid-releasing enzyme (Q9YBQ2) · a predicted model of the same protein · chain C 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 4RE6 · PDBe 4RE6 · UniProt Q9YBQ2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.