3ZMQ

Src-derived mutant peptide inhibitor complex of PTP1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of Accessible Peptidic Tool Compounds to Study the Phosphatase Ptp1B in Intact Cells.

Meyer, C.Hoeger, B.Temmerman, K.Tatarek-Nossol, M.Pogenberg, V.Bernhagen, J.Wilmanns, M.Kapurniotu, A.Kohn, M.

(2014) Acs Chem.Biol. 9: 769

  • DOI: 10.1021/cb400903u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein tyrosine phosphatases (PTPs) play crucial roles in health and disease. Chemical modulators of their activity are vital tools to study their function. An important aspect is the accessibility of these tools, which is usually limited or not exi ...

    Protein tyrosine phosphatases (PTPs) play crucial roles in health and disease. Chemical modulators of their activity are vital tools to study their function. An important aspect is the accessibility of these tools, which is usually limited or not existent due to the required, often complex synthesis of the molecules. We describe here a strategy for the development of cellular active inhibitors and in-cell detection tools for PTP1B as a model PTP, which plays important roles in diabetes, obesity, and cancer. The tool compounds are based on a peptide sequence from PTP1B's substrate Src, and the resulting compounds are commercially accessible through standard peptide synthesis. The peptide inhibitor is remarkably selective against a panel of PTPs. We provide the co-crystal structure of PTP1B with the sequence from Src and the optimized peptide inhibitor, showing the molecular basis of the interaction of PTP1B with part of its natural substrate and explaining the crucial interactions to enhance binding affinity, which are made possible by simple optimization of the sequence. Our approach enables the broad accessibility of PTP1B tools to researchers and has the potential for the systematic development of accessible PTP modulators to enable the study of PTPs.


    Organizational Affiliation

    Genome Biology Unit, European Molecular Biology Laboratory , Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1
A
329Homo sapiensMutation(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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
C
10Homo sapiensMutation(s): 1 
Gene Names: SRC (SRC1)
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Go to Gene View: SRC
Go to UniProtKB:  P12931
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FTY
Query on FTY
C
L-PEPTIDE LINKINGC10 H12 F2 N O5 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.020α = 90.00
b = 61.270β = 90.00
c = 88.690γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references