3D9C | pdb_00003d9c

Crystal Structure PTP1B complex with aryl Seleninic acid

• PDB DOI: https://doi.org/10.2210/pdb3D9C/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-27 Released: 2008-09-23 
• Deposition Author(s): Abdo, M., Liu, S., Zhou, B., Walls, C.D., Knapp, S., Zhang, Z.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 

Literature

Seleninate in place of phosphate: irreversible inhibition of protein tyrosine phosphatases.

Abdo, M., Liu, S., Zhou, B., Walls, C.D., Wu, L., Knapp, S., Zhang, Z.Y.

(2008) J Am Chem Soc 130: 13196-13197

• PubMed: 18781746 
• DOI: https://doi.org/10.1021/ja804489m
• Primary Citation of Related Structures:  
  3D9C


• PubMed Abstract: 
  

  A homotyrosine based seleninic acid irreversibly inhibits protein tyrosine phosphatases by forming a covalent selenosulfide linkage with the active site cysteine sulfhydryl specifically. The details of the event are revealed by model synthetic studies and by kinetic, mass spectrometric, and crystallographic characterization.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.77 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 282 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	321	Homo sapiens	Mutation(s): 0  Gene Names: PTPN1, PTP1B EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
PHAROS:  P18031 GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZYZ	B [auth A]	(4-{(2S)-2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}phenyl)methaneseleninic acid C16 H23 N O6 Se CEUSGDKNGCAEAX-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.279	α = 90
b = 89.279	β = 90
c = 105.656	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-23 
Deposition Author(s): Abdo, M., Liu, S., Zhou, B., Walls, C.D., Knapp, S., Zhang, Z.-Y.

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations