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M9A HCV protease complex with pentapeptide keto-amide inhibitor

Analyse M9A HCV protease complex with pentapeptide keto-amide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RGQ
Type: protein
Length: 379 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NS3 protease; NS4A peptide
EC: 3.4.21.98
UniProt: P27958, O39914
Ligands: AKP, ZN
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NS3 protease (EC 3.4.21.98)	protein	154	11% helix, 49% strand	P27958
B	NS3 protease (EC 3.4.21.98)	protein	186	15% helix, 44% strand	P27958
C	NS4A peptide	protein	22	0% helix, 45% strand	O39914
D	NS4A peptide	protein	17	0% helix, 53% strand	O39914

Ligands and binding sites

AKP · N-(pyrazin-2-ylcarbonyl)leucylisoleucyl-N~1~-{1-[2-({1-carboxy-2-[4-(phosphonooxy)phenyl]ethyl}amino)-1,1-dihydroxy-2-oxoethyl]but-3-enyl}-3-cyclohexylalaninamide · ligand · chains B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

5 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	168	0.60	0.83	27	empty
2	51	0.41	0.82	21	empty
3	74	0.34	0.76	18	empty
4	62	0.33	0.76	17	empty
5	53	0.26	0.74	16	empty

Interfaces

6 interfaces between chains.

B–C · 1342 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 921 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 477 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 340 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 239 Å² buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

1RGQ · M9A HCV Protease complex with pentapeptide keto-amide inhibitor · 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 P27958
Every structure of UniProt O39914
Elsewhere: RCSB PDB 1RGQ · PDBe 1RGQ · UniProt P27958 · UniProt O39914

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