6BQJ: Hepatis C virus protease

Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl sulfonamide inhibitor (compound 16). Determined by X-ray diffraction at 1.69 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Hepatitis C virus
Chains: 3
Atoms: 4,775
Mol. weight: 72.85 kDa
Ligands: ZN, Z1B
Released: 21 Mar 2018

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

Secondary structure: helices and β-sheets

6BQJ contains 24 α-helices and 60 β-strands across 3 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: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	-8	1	1
β-strand	-7--1	7	2
β-strand	6-9	4	2
α-helix	13-22	10
β-strand	24	1	3
α-helix	28-29	2
β-strand	33-37	5	2
β-strand	42-48	7	2
β-strand	51-54	4	2
α-helix	56-59	4
β-strand	64	1	1
β-strand	66	1	3
β-strand	71	1	1
β-strand	75-77	3	2
β-strand	82-86	5	2
α-helix	87-88	2
β-strand	94	1	2
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	172-179	8

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	-8	1	5
β-strand	-7--1	7	6
β-strand	6-9	4	6
α-helix	13-15	3
α-helix	17-22	6
β-strand	24	1	7
α-helix	28-29	2
β-strand	33-37	5	6
β-strand	42-48	7	6
β-strand	51-54	4	6
α-helix	56-59	4
β-strand	64	1	5
β-strand	66	1	7
β-strand	71	1	5
β-strand	75-77	3	6
β-strand	82-86	5	6
α-helix	87-88	2
β-strand	94	1	6
β-strand	96	1	8
β-strand	103-107	5	8
α-helix	108	1
β-strand	113-118	6	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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	-8	1	9
β-strand	-7--1	7	6
β-strand	6-9	4	6
α-helix	13-15	3
α-helix	17-22	6
β-strand	24	1	10
α-helix	28-29	2
β-strand	33-37	5	6
β-strand	42-48	7	6
β-strand	51-54	4	6
α-helix	56-59	4
β-strand	64	1	9
β-strand	66	1	10
β-strand	71	1	9
β-strand	75-77	3	6
β-strand	82-86	5	6
α-helix	87-88	2
β-strand	94	1	6
β-strand	96	1	11
β-strand	103-107	5	11
α-helix	108	1
β-strand	113-118	6	11
β-strand	123-131	9	11
α-helix	132-134	3
α-helix	141	1
β-strand	142-144	3	11
β-strand	150-160	11	11
β-strand	163-171	9	11
α-helix	172-180	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NS3 protease	A, B, C	protein	219	Hepatitis C virus	P27958 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6BQJ_1 NS3 protease (chains A, B, C)
MKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTATQTFLA
TSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTCGSSDLY
LVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAK
AVDFIPVESLETTMRSPAIRAPSTSLRPHSSTTTTTTEI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
Z1B	N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(2S)-1-[(cyclopropylsulfonyl)a…	C39 H49 F2 N5 O9 S	3

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

Primary citation

Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor. Zheng, B., D'Andrea, S.V., Sun, L.Q. et al. ACS Med Chem Lett (2018) 9:143-148. DOI 10.1021/acsmedchemlett.7b00503 · 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)…
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…
2O8M 2.0 Å, Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A protease
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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