7MME: HCV NS3/4A D168A protease

Crystal structure of HCV NS3/4A D168A protease in complex with JZ01-15. Determined by X-ray diffraction at 1.56 Å resolution. Released 31 Aug 2022.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Hepacivirus C
Chains: 1
Atoms: 1,750
Mol. weight: 22.66 kDa
Ligands: ZN, 9H4
Released: 31 Aug 2022

Explore 7MME in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MME contains 9 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: 9 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
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
NS3/4A protease	A	protein	200	Hepacivirus C	P26664 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7MME_1 NS3/4A protease (chains A)
HMASMKKKGSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTATQ
TFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTCGS
SDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVSTR
GVAKAVAFIPVESLETTMRS

Ligands and cofactors

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

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

Primary citation

Deciphering the Molecular Mechanism and Role of Fluorination in HCV Protease Inhibitor Potency and Drug Resistance. Zephyr, J., Nageswara Rao, D. 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
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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