6VDL: HCV NS3/4A protease A156T mutant

HCV NS3/4A protease A156T mutant in complex with glecaprevir. Determined by X-ray diffraction at 1.95 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Hepatitis C virus genotype 1a (isolate 1)
Chains: 1
Atoms: 1,752
Mol. weight: 22.83 kDa
Ligands: O31, ZN
Released: 30 Dec 2020

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

Secondary structure: helices and β-sheets

6VDL contains 10 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: 10 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
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	1172-1178	7

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

>6VDL_1 Non-structural protein 4A, Serine protease NS3 (chains A)
GSHMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTC
GSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRTAVC
TRGVAKAVDFIPVESLETTMRSP

Ligands and cofactors

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

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

Primary citation

RAS at position 156 of HCV NS3/4A protease abolish inhibition by current HCV drugs. Timm, J., Zephyr, J., Hou, S. 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
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
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

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