Research workbench
Structural basis of substrate specificity and protease inhibition in norwalk virus
Analyse Structural basis of substrate specificity and protease inhibition in norwalk… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4INH
- Type
- protein
- Length
- 1,368 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Peptide inhibitor, SYC59
- EC
- 3.6.1.15, 3.4.22.66, 2.7.7.48
- UniProt
- Q83883
- Ligands
- PHQ
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 50% 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 | 172 | 8% helix, 49% strand | Q83883 |
| B | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 170 | 8% helix, 50% strand | Q83883 |
| C | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 166 | 8% helix, 51% strand | Q83883 |
| D | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 167 | 8% helix, 49% strand | Q83883 |
| E, G | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 167 | 8% helix, 51% strand | Q83883 |
| F | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 167 | 8% helix, 49% strand | Q83883 |
| H | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 168 | 8% helix, 51% strand | Q83883 |
| J, M, S, T, N, O, P, Q | Peptide inhibitor, SYC59 | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 8 copies · chains B, J, A, M, C, S, D, T, E, N, F, O, G, P, H, Q
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, E, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.75 | 0.79 | 85 | PHQ |
| 2 | 702 | 0.74 | 0.80 | 66 | PHQ |
| 3 | 242 | 0.66 | 0.83 | 28 | DMS |
| 4 | 294 | 0.65 | 0.81 | 34 | DMS |
| 5 | 342 | 0.61 | 0.78 | 36 | empty |
Interfaces
22 interfaces between chains.
- A–H · 714 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 661 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 487 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 477 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 436 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 4INH · Structural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus · 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 4INH · PDBe 4INH · UniProt Q83883
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.