2O8M: Protease

Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A protease. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Oct 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Hepatitis C virus
Chains: 4
Atoms: 3,013
Mol. weight: 47.43 kDa
Ligands: ZN
Released: 9 Oct 2007

Explore 2O8M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2O8M contains 17 α-helices and 40 β-strands across 4 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: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
α-helix	13-22	10
β-strand	24	1	2
β-strand	33-37	5	1
β-strand	42-48	7	1
β-strand	51-55	5	1
α-helix	56-59	4
β-strand	64	1	3
β-strand	66	1	2
β-strand	71	1	3
β-strand	75-77	3	1
β-strand	82-86	5	1
α-helix	87-88	2
β-strand	94	1	1
β-strand	96	1	4
β-strand	103-107	5	4
α-helix	108	1
β-strand	113-118	6	4
β-strand	123-131	9	4
α-helix	132-134	3
β-strand	142-144	3	4
β-strand	150-160	11	4
β-strand	163-171	9	4
α-helix	172-180	9

Chain B: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	5
β-strand	33-37	5	6
β-strand	42-48	7	6
β-strand	51-55	5	6
α-helix	56-59	4
β-strand	64	1	7
β-strand	71	1	7
β-strand	75-77	3	6
β-strand	82-86	5	6
α-helix	87-88	2
β-strand	91	1	5
α-helix	93	1
β-strand	94	1	6
α-helix	95	1
β-strand	96	1	8
α-helix	97	1
β-strand	103-107	5	8
α-helix	108	1
β-strand	113-120	8	8
β-strand	123-131	9	8
α-helix	132-134	3
β-strand	142-144	3	8
β-strand	150-160	11	8
β-strand	163-171	9	8
α-helix	172-180	9

Chain C: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	221-222	2
β-strand	223	1	3
β-strand	224-230	7	1
β-strand	236-237	2	6
α-helix	238-239	2

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	221-222	2
β-strand	223	1	7
β-strand	224-230	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	200	Hepatitis C virus	P27958 (AlphaFold model)
Protease	C, D	protein	23		P27958 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2O8M_1 Protease (chains A, B)
MASMTGGQQMGAPITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCIN
GVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTR
HADVIPVRRRGDSRGSLLSPRPISYLKGSAGGPLLCPAGHAVGLFRAAVCTRGVAKAVDF
IPVENLETTMRSGSHHHHHH

Sequence of entity 2 (C, D), FASTA

>2O8M_2 Protease (chains C, D)
KKGCVVIVGRIVLSGKPAIIPKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization. Prongay, A.J., Guo, Z., Yao, N. et al. J Med Chem (2007) 50:2310-2318. DOI 10.1021/jm060173k · PubMed

Other PDB entries of the same protein (UniProt P27958 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BZY 1.6 Å, Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423…
5FGB 1.65 Å, Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)…
6BQJ 1.69 Å, Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl…
2XI3 1.7 Å, HCV-H77 NS5B Polymerase Complexed With GTP
4N0Y 1.75 Å, Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic region 314-324 bound to…
2XI2 1.8 Å, HCV-H77 NS5B Apo Polymerase
6UYD 1.9 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from…
5FGC 1.9 Å, Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)…
6BQK 1.97 Å, Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl…
5EOC 1.98 Å, Crystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2…
4XVJ 2.0 Å, Structure of the hepatitis C virus envelope glycoprotein E2 antigenic 2 region 412-423…
4Z0X 2.0 Å, Structure of Hepatitis C Virus Envelope glycoprotein E2 antigenic region 434-446 bound…

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