Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.91 kDa 
• Atom Count: 2997 
• Modelled Residue Count: 290 
• Deposited Residue Count: 291 
• Unique protein chains: 1

2HC1

Engineered catalytic domain of protein tyrosine phosphatase HPTPbeta.

• PDB DOI: 10.2210/pdb2HC1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-06-14 Released: 2006-06-27 
• Deposition Author(s): Evdokimov, A.G., Pokross, M., Walter, R., Mekel, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.179 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

Literature

Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.

Evdokimov, A.G., Pokross, M., Walter, R., Mekel, M., Cox, B., Li, C., Bechard, R., Genbauffe, F., Andrews, R., Diven, C., Howard, B., Rastogi, V., Gray, J., Maier, M., Peters, K.G.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1435-1445

• PubMed: 17139078 
• DOI: 10.1107/S0907444906037784
• Primary Citation of Related Structures:  
  2HC1, 2HC2, 2I3R, 2I3U, 2I4E, 2I4G, 2I4H, 2I5X


• PubMed Abstract: 
  

Protein tyrosine phosphatases (PTPs) play roles in many biological processes and are considered to be important targets for drug discovery. As inhibitor development has proven challenging, crystal structure-based design will be very helpful to advance inhibitor potency and selectivity. Successful application of protein crystallography to drug discovery heavily relies on high-quality crystal structures of the protein of interest complexed with pharmaceutically interesting ligands. It is very important to be able to produce protein-ligand crystals rapidly and reproducibly for as many ligands as necessary. This study details our efforts to engineer the catalytic domain of human protein tyrosine phosphatase beta (HPTPbeta-CD) with properties suitable for rapid-turnaround crystallography. Structures of apo HPTPbeta-CD and its complexes with several novel small-molecule inhibitors are presented here for the first time.

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Organizational Affiliation: 

Structural Biology, Procter and Gamble Pharmaceuticals, 8700 Mason-Montgomery Road, Mason, OH 45140, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase beta	A	291	Homo sapiens	Mutation(s): 2  Gene Names: PTPRB, PTPB EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P23467 (Homo sapiens) Explore P23467  Go to UniProtKB:  P23467
PHAROS:  P23467 GTEx:  ENSG00000127329

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.179 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.06	α = 90
b = 70.714	β = 90
c = 118.455	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-14 
• Released Date: 2006-06-27 
Deposition Author(s): Evdokimov, A.G., Pokross, M., Walter, R., Mekel, M.

Revision History  

• Version 1.0: 2006-06-27
  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: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations