Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 37.90 kDa 
• Atom Count: 2735 
• Modelled Residue Count: 298 
• Deposited Residue Count: 321 
• Unique protein chains: 1

1PTY

CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH TWO PHOSPHOTYROSINE MOLECULES

• PDB DOI: 10.2210/pdb1PTY/pdb

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


• Deposited: 1997-01-16 Released: 1998-01-21 
• Deposition Author(s): Zhao, Y., Puius, Y.A., Sullivan, M., Lawrence, D., Almo, S.C., Zhang, Z.-Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Literature

Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design.

Puius, Y.A., Zhao, Y., Sullivan, M., Lawrence, D.S., Almo, S.C., Zhang, Z.Y.

(1997) Proc Natl Acad Sci U S A 94: 13420-13425

• PubMed: 9391040 
• DOI: 10.1073/pnas.94.25.13420
• Primary Citation of Related Structures:  
  1AAX, 1PTY


• PubMed Abstract: 
  

The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 microM), and the structure was refined to an R-factor of 18. 2% at 1.9 A resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1% at 1.85 A. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.

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Related Citations: 

• Potent Low Molecular Weight Substrates for Protein-Tyrosine Phosphatase
  Montserat, J., Chen, L., Lawrence, D.S., Zhang, Z.Y.
  (1996) J Biol Chem 271: 7868

• Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B
  Jia, Z., Barford, D., Flint, A.J., Tonks, N.K.
  (1995) Science 268: 1754

• Crystal Structure of Human Protein Tyrosine Phosphatase 1B
  Barford, D., Flint, A.J., Tonks, N.K.
  (1994) Science 263: 1397

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN TYROSINE PHOSPHATASE 1B	A	321	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTR	C [auth A], D [auth A]	O-PHOSPHOTYROSINE C9 H12 N O6 P DCWXELXMIBXGTH-QMMMGPOBSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.909	α = 90
b = 87.909	β = 90
c = 103.822	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-01-16 
• Released Date: 1998-01-21 
Deposition Author(s): Zhao, Y., Puius, Y.A., Sullivan, M., Lawrence, D., Almo, S.C., Zhang, Z.-Y.

Revision History  

• Version 1.0: 1998-01-21
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other