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HCV NS3 protease domain with NS4A peptide and a ketoamide inhibitor with a P2 norborane

Analyse HCV NS3 protease domain with NS4A peptide and a ketoamide inhibitor with a P2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F9U
Type: protein
Length: 377 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NS3 PROTEASE/HELICASE'; Polyprotein
UniProt: Q91RS4
Ligands: 5NH, ZN
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NS3 PROTEASE/HELICASE'	protein	183	15% helix, 44% strand	Q91RS4
B	Polyprotein	protein	23	0% helix, 43% strand	—
C	NS3 PROTEASE/HELICASE'	protein	152	12% helix, 50% strand	—
D	Polyprotein	protein	19	0% helix, 47% strand	—

Ligands and binding sites

5NH · 1,1-dimethylethyl [1-cyclohexyl-2-[3-[[[1-[2-[[2-[[2-(dimethylamino)-2-oxo-1-phenylethyl]amino]-2-oxoethyl]amino]-1,2-dioxoethyl]pentyl]amino]carbonyl]-2-azabicyclo[2.2.1]heptan-2-yl]-2-oxoethyl]carbamate · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	92	0.58	0.87	19	empty
2	61	0.39	0.80	15	empty
3	64	0.35	0.78	15	empty
4	56	0.31	0.76	17	empty

Interfaces

6 interfaces between chains.

A–B · 1316 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 878 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 433 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 335 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 332 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2F9U · HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with a P2 norborane · 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 Q91RS4
Elsewhere: RCSB PDB 2F9U · PDBe 2F9U · UniProt Q91RS4

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