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Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl sulfonamide inhibitor (compound 16)

Analyse Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BQJ
Type: protein
Length: 595 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NS3 protease
UniProt: A0A075D220
Ligands: Z1B, ZN, CL
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NS3 protease	protein	194	13% helix, 44% strand	A0A075D220
B	NS3 protease	protein	194	13% helix, 44% strand	A0A075D220
C	NS3 protease	protein	207	12% helix, 41% strand	A0A075D220

Ligands and binding sites

Z1B · N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(2S)-1-[(cyclopropylsulfonyl)amino]-4,4-difluoro-1-oxobutan-2-yl}-4-[(7-methoxy-2-phenylquinolin-4-yl) oxy]-L-prolinamide · ligand · 3 copies · chains A, B, C
ZN · Zinc ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 6 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	793	0.68	0.75	89	ACT
2	124	0.54	0.82	25	ACT
3	102	0.51	0.82	21	empty
4	197	0.48	0.76	37	empty
5	51	0.29	0.75	16	empty

Interfaces

3 interfaces between chains.

B–C · 448 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 262 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 190 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6BQJ · Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl… · 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 A0A075D220
Elsewhere: RCSB PDB 6BQJ · PDBe 6BQJ · UniProt A0A075D220

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