Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization, gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: assay for oligomerization, gel filtration

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.93 kDa 
• Atom Count: 3054 
• Residue Count: 369 
• Unique protein chains: 1

5V5E

Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 733)

• DOI: 10.2210/pdb5V5E/pdb

• Classification: VIRAL PROTEIN / INHIBITOR
• Organism(s): Human gammaherpesvirus 8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-14 Released: 2017-04-12 
• Deposition Author(s): Thompson, M.C., Acker, T.M., Fraser, J.S., Craik, C.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.230 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.

Acker, T.M., Gable, J.E., Bohn, M.F., Jaishankar, P., Thompson, M.C., Fraser, J.S., Renslo, A.R., Craik, C.S.

(2017) J Am Chem Soc 139: 11650-11653

• PubMed: 28759216 
• DOI: 10.1021/jacs.7b04030
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we sought to dissect a putative allosteric network linking a cryptic site at the dimerization interface to enzyme function. Five cryogenic X-ray structures were solved of the monomeric protease with allosteric inhibitors bound to the dimer interface site. Distinct coordinated movements captured by the allosteric inhibitors were also revealed as alternative states in room-temperature X-ray data and comparative analyses of other dimeric herpesvirus proteases. A two-step mechanism was elucidated through detailed kinetic analyses and suggests an enzyme isomerization model of inhibition. Finally, a representative allosteric inhibitor from this class was shown to be efficacious in a cellular model of viral infectivity. These studies reveal a coordinated dynamic network of atomic communication linking cryptic binding site occupancy and allosteric inactivation of KHSV Pr that can be exploited to target other members of this clinically relevant family of enzymes.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ORF 17	A, B	193	Human gammaherpesvirus 8	Mutation(s): 0  Gene Names: ORF17 EC: 3.4.21.97
Find proteins for O40922 (Human herpesvirus 8) Go to UniProtKB:  O40922

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8N4	A, B	4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-{[3-(trifluoromethoxy)phenyl]amino}benzoic acid C27 H26 F3 N3 O4 OQQHKPTYNRWLGC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.230 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.4	α = 90
b = 96.84	β = 90
c = 119.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-14 
• Released Date: 2017-04-12 
Deposition Author(s): Thompson, M.C., Acker, T.M., Fraser, J.S., Craik, C.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI090592
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1F32GM111012
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	5F32HL129989-03

Revision History 

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence