Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 37896.21 
• Atom Count: 2472 
• Residue Count: 321 
• Unique protein chains: 1

1PTY

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

• DOI: 10.2210/pdb1PTY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Work: 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.USA 94: 13420-13425

• PubMed: 9391040 
• Primary Citation of Related Structures:  
  1AAX


• 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.

---

Related Citations: 

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




---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN TYROSINE PHOSPHATASE 1B	A	321	Homo sapiens	Mutation(s): 1  Gene Names: PTPN1 (PTP1B) EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens) Go to Gene View: PTPN1 Go to UniProtKB:  P18031

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
PTR	A	O-PHOSPHOTYROSINE PHOSPHONOTYROSINE C9 H12 N O6 P DCWXELXMIBXGTH-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 87.909	α = 90.00
b = 87.909	β = 90.00
c = 103.822	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance