5QF1

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000272b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.844 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Keedy, D.A.Hill, Z.B.Biel, J.T.Kang, E.Rettenmaier, T.J.Brandao-Neto, J.Pearce, N.M.von Delft, F.Wells, J.A.Fraser, J.S.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.36307
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. ...

    Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function.


    Organizational Affiliation

    Crystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.,Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.,Diamond Light Source, Didcot, United Kingdom.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 1
A
321Homo sapiensMutation(s): 2 
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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JMD
Query on JMD

Download SDF File 
Download CCD File 
A
4-(2-hydroxyethyl)benzonitrile
C9 H9 N O
RBSJBNYPTGMZIH-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.844 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.322α = 90.00
b = 90.322β = 90.00
c = 106.740γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references, Structure summary