6P6R: Non-structural protein 4A,Serine protease NS3

HCV NS3/4A protease domain of genotype 1a3a chimera in complex with glecaprevir. Determined by X-ray diffraction at 1.75 Å resolution. Released 10 Jun 2020.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Hepatitis C virus genotype 1a (isolate 1)
Chains: 1
Atoms: 1,882
Mol. weight: 22.72 kDa
Ligands: ZN, O31
Released: 10 Jun 2020

Explore 6P6R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P6R contains 11 α-helices and 22 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	983-985	3
β-strand	992	1	1
β-strand	993-999	7	2
β-strand	1006-1009	4	2
α-helix	1013-1022	10
β-strand	1024	1	3
α-helix	1028-1029	2
β-strand	1031	1	4
β-strand	1033-1037	5	2
β-strand	1042-1048	7	2
β-strand	1051-1055	5	2
α-helix	1056-1059	4
β-strand	1064	1	1
β-strand	1066	1	3
β-strand	1071	1	1
β-strand	1075-1077	3	2
α-helix	1078-1080	3
β-strand	1082-1086	5	2
α-helix	1087-1088	2
β-strand	1091	1	4
β-strand	1094	1	2
α-helix	1095	1
β-strand	1096	1	5
α-helix	1097	1
β-strand	1103-1107	5	5
β-strand	1113-1118	6	5
β-strand	1123-1131	9	5
α-helix	1132-1134	3
α-helix	1141	1
β-strand	1142-1144	3	5
β-strand	1150-1160	11	5
β-strand	1163-1171	9	5
α-helix	1172-1180	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 4A,Serine protease NS3	A	protein	203	Hepatitis C virus genotype 1a (isolate 1)	P26664 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6P6R_1 Non-structural protein 4A,Serine protease NS3 (chains A)
GSHMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTC
GSSDLYLVTRHADVIPVRRRGDSTGSLLSPRPLSYLKGSSGGPLLCPAGHAVGIFRAAVS
TRGVAKAVQFIPVESLETTMRSP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
O31	Glecaprevir	C38 H46 F4 N6 O9 S	1

Water and common crystallization additives (EDO, SO4, CL) are not listed.

Primary citation

Molecular mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir and characterization of genotype-specific structural differences. Timm, J., Kosovrasti, K., Henes, M. et al. To be published.

Other PDB entries of the same protein (UniProt P26664 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RC4 1.5 Å, Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
3HKW 1.55 Å, HCV NS5B genotype 1a in complex with 1,5 benzodiazepine inhibitor 6
7MME 1.56 Å, Crystal structure of HCV NS3/4A D168A protease in complex with JZ01-15
3RC5 1.6 Å, Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
7MMA 1.65 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-145
7MML 1.7 Å, Crystal structure of HCV NS3/4A D168A protease in complex with NR01-145
6P6L 1.73 Å, HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir
7MM3 1.78 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-127
5VOJ 1.8 Å, Crystal structure of HCV NS3/4A protease in complex with JZ01-15, an analogue of…
3QGI 1.8 Å, Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a…
5VP9 1.86 Å, Crystal structure of HCV NS3/4A protease in complex with AM-07, an analogue of 5172-mcP1P3
7MM4 1.89 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-115

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