Research workbench
1.85 a resolution structure of norovirus 3CL protease in complex with inhibitor 7D
Analyse 1.85 a resolution structure of norovirus 3CL protease in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W5J
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like protease
- EC
- 3.4.22.66
- UniProt
- Q83883
- Ligands
- TKS
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like protease (EC 3.4.22.66) | protein | 170 | 6% helix, 51% strand | Q83883 |
| B | 3C-like protease (EC 3.4.22.66) | protein | 159 | 6% helix, 53% strand | Q83883 |
Ligands and binding sites
- TKS · 2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}amino)-1-oxopropan-2-yl]carbamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.63 | 0.80 | 34 | empty |
| 2 | 63 | 0.30 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 478 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6W5J · 1.85 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7d · 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 Q83883
- Elsewhere: RCSB PDB 6W5J · PDBe 6W5J · UniProt Q83883
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