Research workbench
A mechanistic view of enzyme inhibition and peptide hydrolysis in the active site of the SARS-cov 3C-like peptidase
Analyse A mechanistic view of enzyme inhibition and peptide hydrolysis in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z3D
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB (PP1AB); Inhibitor
- EC
- 3.4.22.-
- UniProt
- P59641
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB (PP1AB) (EC 3.4.22.-) | protein | 306 | 25% helix, 29% strand | P59641 |
| I | Inhibitor | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.39 | 0.75 | 23 | empty |
| 2 | 53 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–I · 423 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2Z3D · A Mechanistic view of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the… · 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 P59641
- Elsewhere: RCSB PDB 2Z3D · PDBe 2Z3D · UniProt P59641
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