MolNFT v1 · #134510 · protein
2.10 a resolution structure of norovirus 3CL protease in complex with the dipeptidyl inhibitor 7L (hexagonal form)
5T6D · Genome polyprotein: “2.10 a resolution structure of norovirus 3CL protease in complex with the dipeptidyl inhibitor 7L (hexagonal…”. X-ray diffraction, 1 ligand (N38), 3 pockets (best druggability 0.64). MolNFT v1 #134510 on…
- PDB
- 5T6D
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.6.1.15, 3.4.22.66, 2.7.7.48
- UniProt
- Q83883
- Ligands
- N38
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 174 | 6% helix, 48% strand | Q83883 |
| B | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 161 | 6% helix, 54% strand | Q83883 |
Ligands and binding sites
- N38 · 3-cyclohexyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-{[3-(4-methoxyphenoxy) propyl]sulfonyl}-L-alaninamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.64 | 0.78 | 53 | N38 |
| 2 | 200 | 0.59 | 0.81 | 31 | empty |
| 3 | 134 | 0.43 | 0.76 | 24 | N38 |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5T6D · 2.10 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl… · 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 5T6D · PDBe 5T6D · UniProt Q83883
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