2P4D | pdb_00002p4d

Structure-assisted discovery of Variola major H1 phosphatase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2P4D/pdb

• Classification: HYDROLASE
• Organism(s): Variola virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-03-12 Released: 2007-05-29 
• Deposition Author(s): Phan, J., Tropea, J.E., Waugh, D.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structure-assisted discovery of variola major H1 phosphatase inhibitors

Phan, J., Tropea, J.E., Waugh, D.S.

(2007) Acta Crystallogr D Biol Crystallogr D63: 698-704

• PubMed: 17505108 
• DOI: https://doi.org/10.1107/S0907444907014904
• Primary Citation Related Structures: 
  2P4D


• PubMed Abstract: 
  

  Variola major virus, the causative agent of smallpox, encodes the dual-specificity H1 phosphatase. Because this enzyme is essential for the production of mature virus particles, it is an attractive molecular target for the development of therapeutic countermeasures for this potential agent of bioterrorism. As a first step in this direction, the crystal structure of H1 phosphatase has been determined at a resolution of 1.8 A. In silico screening methods have led to the identification of several small molecules that inhibit Variola H1 phosphatase with IC(50) values in the low micromolar range. These molecules provide novel leads for future drug development.

---

Organizational Affiliation: 
• Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.24 kDa 
• Atom Count: 1,506 
• Modeled Residue Count: 163 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase	A	172	Variola virus	Mutation(s): 8  EC: 3.1.3.48 (PDB Primary Data), 3.1.3.16 (PDB Primary Data), 3.1.3 (UniProt)
UniProt
Find proteins for P0DOQ5 (Variola virus (isolate Human/India/Ind3/1967)) Explore P0DOQ5  Go to UniProtKB:  P0DOQ5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.441	α = 90
b = 101.441	β = 90
c = 95.101	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Phan, J., Tropea, J.E., Waugh, D.S.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary