5VOJ: HCV NS3/4A protease

Crystal structure of HCV NS3/4A protease in complex with JZ01-15, an analogue of 5172-mcP1P3. Determined by X-ray diffraction at 1.8 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Hepatitis C virus subtype 1a
Chains: 1
Atoms: 1,705
Mol. weight: 22.42 kDa
Ligands: 9H4, ZN
Released: 21 Jun 2017

Explore 5VOJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VOJ 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
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
α-helix	1093	1
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	1172-1178	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NS4A cofactor -- NS3 protein chimera	A	protein	203	Hepatitis C virus subtype 1a	P26664 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VOJ_1 NS4A cofactor -- NS3 protein chimera (chains A)
GSHMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTC
GSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVS
TRGVAKAVDFIPVESLETTMRSP

Ligands and cofactors

ID	Name	Formula	Copies
9H4	tert-butyl [(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)ox…	C37 H50 N6 O9 S	1
ZN	Zinc ion	Zn	1

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

Primary citation

Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants. Matthew, A.N., Zephyr, J., Hill, C.J. et al. J Med Chem (2017) 60:5699-5716. DOI 10.1021/acs.jmedchem.7b00426 · PubMed

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
6P6R 1.75 Å, HCV NS3/4A protease domain of genotype 1a3a chimera in complex with glecaprevir
7MM3 1.78 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-127
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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