6VDM | pdb_00006vdm

HCV NS3/4A protease A156T, D168E double mutant in complex with glecaprevir

• PDB DOI: https://doi.org/10.2210/pdb6VDM/pdb

• Classification: VIRAL PROTEIN, Hydrolase
• Organism(s): Hepatitis C virus (isolate 1)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-12-27 Released: 2020-12-30 
• Deposition Author(s): Timm, J., Schiffer, C.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

RAS at position 156 of HCV NS3/4A protease abolish inhibition by current HCV drugs

Timm, J., Zephyr, J., Hou, S., Kurt Yilmaz, N., Schiffer, C.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.85 kDa 
• Atom Count: 1,771 
• Modelled Residue Count: 202 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 4A, Serine protease NS3	A	203	Hepatitis C virus (isolate 1)	Mutation(s): 17  EC: 3.4.22 (PDB Primary Data), 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1)) Explore P26664  Go to UniProtKB:  P26664

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O31 (Subject of Investigation/LOI)	C [auth A]	Glecaprevir C38 H46 F4 N6 O9 S MLSQGNCUYAMAHD-ITNVBOSISA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
O31	BindingDB:  6VDM	Ki: min: 0.05, max: 0.5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.337	α = 90
b = 58.643	β = 90
c = 60.056	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Timm, J., Schiffer, C.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI085051

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-01-29
  Changes: Derived calculations, Structure summary