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An episulfide cation (thiiranium ring) trapped in the active site of hav 3C proteinase inactivated by peptide-based ketone inhibitors
Analyse An episulfide cation (thiiranium ring) trapped in the active site of hav 3C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H9H
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatitis a virus protease 3C; Three residue peptide
- EC
- 3.4.22.28
- UniProt
- P06441
- Ligands
- ACE, BBL, CF0
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatitis a virus protease 3C (EC 3.4.22.28) | protein | 212 | 18% helix, 50% strand | P06441 |
| I | Three residue peptide | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, I
- BBL · N-[(benzyloxy)carbonyl]-L-alanine · ligand · chains A
- CF0 · Fluoromethane · ion · chains A, I
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 | 138 | 0.48 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–I · 441 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2H9H · An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase… · the same entry in another collection · chain A 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 P06441
- Elsewhere: RCSB PDB 2H9H · PDBe 2H9H · UniProt P06441
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