Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 48.08 kDa 
• Atom Count: 2856 
• Modelled Residue Count: 379 
• Deposited Residue Count: 444 
• Unique protein chains: 2

1RGQ

M9A HCV Protease complex with pentapeptide keto-amide inhibitor

• PDB DOI: 10.2210/pdb1RGQ/pdb

• Classification: Viral protein, hydrolase
• Organism(s): Hepacivirus C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-12 Released: 2004-10-19 
• Deposition Author(s): Liu, Y., Stoll, V.S., Richardson, P.L., Saldivar, A., Klaus, J.L., Molla, A., Kohlbrenner, W., Kati, W.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.312 
• R-Value Work: 0.279 

Literature

Hepatitis C NS3 protease inhibition by peptidyl-alpha-ketoamide inhibitors: kinetic mechanism and structure.

Liu, Y., Stoll, V.S., Richardson, P.L., Saldivar, A., Klaus, J.L., Molla, A., Kohlbrenner, W., Kati, W.M.

(2004) Arch Biochem Biophys 421: 207-216

• PubMed: 14984200 
• DOI: 10.1016/j.abb.2003.11.013
• Primary Citation of Related Structures:  
  1RGQ


• PubMed Abstract: 
  

A series of novel peptidyl-alpha-ketoamide compounds were evaluated as inhibitors of the deltaNS3-NS4A serine protease from the hepatitis C virus. These peptidyl-alpha-ketoamide inhibitors with Ki values ranging from 0.17 nM to 5.6 microM exhibited slow-binding inhibition. Kinetic studies established one-step kinetic mechanisms and dissociation rate constants in the 3-7 x 10(-5) s(-1) range for these compounds. The association rate constants, which ranged from 10 to 263,000 M(-1) s(-1), were responsible for the greater than four order of magnitude overall binding affinity range exhibited by this series. An X-ray crystal structure of a protease-inhibitor complex revealed an unusual interaction between the oxyanion of the adduct and the protein as well as a significant movement in the S1' region of the protein loop comprising residues 35-42. These results are quite different from peptidyl-alpha-ketoacid inhibition of HCV protease, which reportedly undergoes no notable conformational changes and proceeds with a two-step slow-binding kinetic mechanism.

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Organizational Affiliation: 

Antiviral Research, Infectious Disease Research and Advanced Technology, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064-6217, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 Protease	A, B	200	Hepacivirus C	Mutation(s): 0  EC: 3.4.21.98 (PDB Primary Data), 3.4.22 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P27958 (Hepatitis C virus genotype 1a (isolate H77)) Explore P27958  Go to UniProtKB:  P27958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS4A peptide	C, D	22	N/A	Mutation(s): 0
UniProt
Find proteins for O39914 (Hepacivirus C) Explore O39914  Go to UniProtKB:  O39914

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKP	G [auth B]	N-(PYRAZIN-2-YLCARBONYL)LEUCYLISOLEUCYL-N~1~-{1-[2-({1-CARBOXY-2-[4-(PHOSPHONOOXY)PHENYL]ETHYL}AMINO)-1,1-DIHYDROXY-2-OXOETHYL]BUT-3-ENYL}-3-CYCLOHEXYLALANINAMIDE C41 H60 N7 O13 P NANINTGNSYDVAR-PBWGIQFFSA-N
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.312 
• R-Value Work: 0.279 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 226.385	α = 90
b = 226.385	β = 90
c = 76.864	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNX	refinement
HKL-2000	data reduction
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-12 
• Released Date: 2004-10-19 
Deposition Author(s): Liu, Y., Stoll, V.S., Richardson, P.L., Saldivar, A., Klaus, J.L., Molla, A., Kohlbrenner, W., Kati, W.M.

Revision History  

• Version 1.0: 2004-10-19
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance