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2.1 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7g
Analyse 2.1 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
- 6W5L
- Type
- protein
- Length
- 660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Norwalk virus (strain GI/Human/United States/Norwalk/1968)
- Molecule
- 3C-like protease
- EC
- 3.6.1.15, 3.4.22.66, 2.7.7.48
- UniProt
- Q83883
- Ligands
- T0D
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like protease (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 165 | 6% helix, 53% strand | Q83883 |
| B | 3C-like protease (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 166 | 6% helix, 51% strand | Q83883 |
| C | 3C-like protease (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 162 | 7% helix, 52% strand | Q83883 |
| D | 3C-like protease (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 167 | 6% helix, 51% strand | Q83883 |
Ligands and binding sites
- T0D · (2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.62 | 0.81 | 30 | empty |
| 2 | 273 | 0.62 | 0.80 | 31 | empty |
| 3 | 71 | 0.34 | 0.76 | 17 | T0D |
| 4 | 55 | 0.30 | 0.75 | 17 | T0D |
| 5 | 52 | 0.28 | 0.75 | 16 | T0D |
Interfaces
3 interfaces between chains.
- C–D · 460 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 447 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6W5L · 2.1 a resolution structure of norovirus 3CL protease in complex with inhibitor 7G · 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 6W5L · PDBe 6W5L · UniProt Q83883
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