3KF2

The HCV NS3/NS4A protease apo structure

PDB DOI: https://doi.org/10.2210/pdb3KF2/pdb

Classification: HYDROLASE
Organism(s): Hepacivirus hominis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-10-27 Released: 2010-03-09
Deposition Author(s): Lindberg, J.D., Nystrom, S., Cummings, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Induced-Fit Binding of the Macrocyclic Noncovalent Inhibitor TMC435 to its HCV NS3/NS4A Protease Target

Cummings, M.D., Lindberg, J.D., Lin, T.-I., de Kock, H., Lenz, O., Lilja, E., Fellander, S., Baraznenok, V., Nystrom, S., Nilsson, M., Vrang, L., Edlund, M., Rosenquist, A., Samuelsson, B., Raboisson, P., Simmen, K.

(2010) Angew Chem Int Ed Engl 49: 1652-1655

PubMed: 20166108 Search on PubMed
DOI: https://doi.org/10.1002/anie.200906696
Primary Citation of Related Structures:
3KEE, 3KF2

Organizational Affiliation

Tibotec BVBA, Gen De Wittelaan L 11B 3, 2800 Mechelen, Belgium. mcummin1@its.jnj.com

Macromolecule Content

Total Structure Weight: 47.39 kDa
Atom Count: 2,782
Modelled Residue Count: 372
Deposited Residue Count: 446
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A, C [auth B]	200	Hepacivirus hominis	Mutation(s): 1 EC: 3.4.21.98
UniProt
Find proteins for B2Y2M9 (Hepacivirus hominis) Explore B2Y2M9 Go to UniProtKB: B2Y2M9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2Y2M9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
19-mer peptide from Genome polyprotein	B [auth C], D	23	Hepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for Q6GYR8 (Hepacivirus hominis) Explore Q6GYR8 Go to UniProtKB: Q6GYR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6GYR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.924	α = 90
b = 224.924	β = 90
c = 75.545	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.