1AT3 | pdb_00001at3

HERPES SIMPLEX VIRUS TYPE II PROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.291 (Depositor) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex.

Hoog, S.S.Smith, W.W.Qiu, X.Janson, C.A.Hellmig, B.McQueney, M.S.O'Donnell, K.O'Shannessy, D.DiLella, A.G.Debouck, C.Abdel-Meguid, S.S.

(1997) Biochemistry 36: 14023-14029

  • DOI: https://doi.org/10.1021/bi9712697
  • Primary Citation Related Structures: 
    1AT3

  • PubMed Abstract: 

    Human herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) are responsible for herpes labialis (cold sores) and genital herpes, respectively. They encode a serine protease that is required for viral replication, and represent a viable target for therapeutic intervention. Here, we report the crystal structures of HSV-1 and HSV-2 proteases, the latter in the presence and absence of the covalently bound transition state analog inhibitor diisopropyl phosphate (DIP). The HSV-1 and HSV-2 protease structures show a fold that is neither like chymotrypsin nor like subtilisin, and has been seen only in the recently determined cytomegalovirus (CMV) and varicella-zoster virus (VZV) protease structures. HSV-1 and HSV-2 proteases share high sequence homology and have almost identical three-dimensional structures. However, structural differences are observed with the less homologous CMV protease, offering a structural basis for herpes virus protease ligand specificity. The bound inhibitor identifies the oxyanion hole of these enzymes and defines the active site cavity.


  • Organizational Affiliation
    • Department of Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA.

Macromolecule Content 

  • Total Structure Weight: 54.44 kDa 
  • Atom Count: 3,356 
  • Modeled Residue Count: 434 
  • Deposited Residue Count: 494 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HERPES SIMPLEX VIRUS TYPE II PROTEASE
A, B
247Human alphaherpesvirus 2Mutation(s): 0 
UniProt
Find proteins for Q69527 (Human herpesvirus 2)
Explore Q69527 
Go to UniProtKB:  Q69527
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ69527
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DFP

Query on DFP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
DIISOPROPYL PHOSPHONATE
C6 H15 O3 P
BLKXLEPPVDUHBY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.291 (Depositor) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.72α = 90
b = 87.43β = 90
c = 77.28γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XDSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection, Other
  • Version 1.4: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Data collection, Structure summary