3RC4: NS3/4A Protease

Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease. Determined by X-ray diffraction at 1.5 Å resolution. Released 4 May 2011.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Hepatitis C virus subtype 1a, Homo sapiens
Chains: 2
Atoms: 1,645
Mol. weight: 22.92 kDa
Ligands: ZN
Released: 4 May 2011

Explore 3RC4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RC4 contains 13 α-helices and 23 β-strands across 2 chains. 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: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	983-985	3
α-helix	989-991	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	1051-1054	4	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
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
α-helix	1108	1
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	1172-1179	8

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4-6	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NS3/4A Protease	A	protein	203	Hepatitis C virus subtype 1a	P26664 (AlphaFold model)
Product TRIF	B	protein	13	Homo sapiens	Q8IUC6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3RC4_1 NS3/4A Protease (chains A)
GSHMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTC
GSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSAGGPLLCPAGHAVGIFRAAVS
TRGVAKAVDFIPVESLETTMRSP

Sequence of entity 2 (B), FASTA

>3RC4_2 Product TRIF (chains B)
PPPPPPPPSSTPC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease. Romano, K.P., Laine, J.M., Deveau, L.M. et al. J Virol (2011) 85:6106-6116. DOI 10.1128/JVI.00377-11 · PubMed

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

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
7MM4 1.89 Å, Crystal structure of HCV NS3/4A protease in complex with NR01-115

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