MolNFT v1 · #26494 · protein
Crystal structure of norovirus 3C-like protease
1WQS: “Crystal structure of norovirus 3C-like protease”. X-ray diffraction, 1 ligand (HG), 7 pockets (best druggability 0.65). MolNFT v1 #26494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WQS
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like protease
- UniProt
- Q9DU47
- Ligands
- HG
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3C-like protease | protein | 173 | 8% helix, 43% strand | Q9DU47 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 8 copies · chains A, B, C, D
- TAR · D(-)-tartaric acid · additive · chains A
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.65 | 0.80 | 49 | empty |
| 2 | 390 | 0.60 | 0.76 | 34 | empty |
| 3 | 178 | 0.52 | 0.78 | 32 | empty |
| 4 | 135 | 0.48 | 0.79 | 33 | empty |
| 5 | 112 | 0.43 | 0.77 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1068 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 945 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 798 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 743 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1WQS · Crystal structure of Norovirus 3C-like protease · 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 Q9DU47
- Elsewhere: RCSB PDB 1WQS · PDBe 1WQS · UniProt Q9DU47
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