6VDL | pdb_00006vdl

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

PDB DOI: https://doi.org/10.2210/pdb6VDL/pdb

Classification: VIRAL PROTEIN
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.200 (Depositor), 0.198 (DCC)
R-Value Work:
0.152 (Depositor), 0.153 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 22.83 kDa
Atom Count: 1,752
Modeled Residue Count: 200
Deposited Residue Count: 203
Unique protein chains: 1

Macromolecules

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| 3D Structure

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): 16 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26664
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O31 (Subject of Investigation/LOI) Query on O31 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Glecaprevir C₃₈ H₄₆ F₄ N₆ O₉ S MLSQGNCUYAMAHD-ITNVBOSISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.200 (Depositor), 0.198 (DCC)
R-Value Work: 0.152 (Depositor), 0.153 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.793	α = 90
b = 58.601	β = 90
c = 59.89	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-30

Deposition Author(s):

Timm, J.

Schiffer, C.A.

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

Revision History (Full details and data files)

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