Research workbench
X-ray structure at 1.75 a resolution of a norovirus protease linked to an active site directed peptide inhibitor
Analyse X-ray structure at 1.75 a resolution of a norovirus protease linked to an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IPH
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiol protease P3C
- EC
- 3.4.22.-
- UniProt
- Q04544
- Ligands
- LGG
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiol protease P3C (EC 3.4.22.-) | protein | 180 | 6% helix, 49% strand | Q04544 |
| B | Thiol protease P3C (EC 3.4.22.-) | protein | 177 | 6% helix, 50% strand | Q04544 |
Ligands and binding sites
- LGG · N-acetyl-L-alpha-glutamyl-L-phenylalanyl-L-glutaminyl-N-[(1S)-4-amino-1-(2-carboxyethyl)-4-oxobutyl]-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.50 | 0.77 | 34 | LGG |
| 2 | 155 | 0.48 | 0.77 | 29 | LGG |
| 3 | 84 | 0.40 | 0.78 | 19 | empty |
| 4 | 66 | 0.33 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 757 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2IPH · X-ray Structure at 1.75 A Resolution of a Norovirus Protease Linked to an Active Site… · 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 Q04544
- Elsewhere: RCSB PDB 2IPH · PDBe 2IPH · UniProt Q04544
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