Research workbench
1.85 a resolution structure of norovirus 3CL protease in complex with inhibitor 5D
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
- 6W5H
- Type
- protein
- Length
- 663 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like protease
- EC
- 3.4.22.66
- UniProt
- Q83883
- Ligands
- TKP
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like protease (EC 3.4.22.66) | protein | 168 | 7% helix, 52% strand | Q83883 |
| B | 3C-like protease (EC 3.4.22.66) | protein | 167 | 6% helix, 52% strand | Q83883 |
| C | 3C-like protease (EC 3.4.22.66) | protein | 163 | 6% helix, 53% strand | Q83883 |
| D | 3C-like protease (EC 3.4.22.66) | protein | 165 | 7% helix, 52% strand | Q83883 |
Ligands and binding sites
- TKP · 2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.64 | 0.80 | 33 | empty |
| 2 | 248 | 0.61 | 0.80 | 31 | empty |
| 3 | 122 | 0.37 | 0.73 | 28 | empty |
| 4 | 55 | 0.32 | 0.76 | 15 | empty |
| 5 | 68 | 0.31 | 0.75 | 19 | TKP |
Interfaces
3 interfaces between chains.
- C–D · 441 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 160 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 6W5H · 1.85 A resolution structure of Norovirus 3CL protease in complex with inhibitor 5d · 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 6W5H · PDBe 6W5H · UniProt Q83883
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.