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2.35A resolution structure of norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (21-mer) inhibitor
Analyse 2.35A resolution structure of norovirus 3CL protease in complex an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DG6
- Type
- protein
- Length
- 322 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
- V66, CL
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like protease (EC 3.4.22.66) | protein | 165 | 8% helix, 50% strand | Q83883 |
| B | 3C-like protease (EC 3.4.22.66) | protein | 157 | 6% helix, 49% strand | Q83883 |
Ligands and binding sites
- V66 · tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-23-oxa-6,9,14,21,22-pentaazabicyclo[18.2.1]tricosa-1(22),20-dien-4-yl]carbamate · ligand · chains A
- CL · Chloride ion · ion · 3 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 | 229 | 0.64 | 0.82 | 28 | CL |
| 2 | 63 | 0.33 | 0.76 | 16 | V66 |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5DG6 · 2.35A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell… · 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 5DG6 · PDBe 5DG6 · UniProt Q83883
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