5QDF

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000295a

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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:  
    6B8E, 6B8T, 6B95, 6B8X, 6B8Z, 6B90, 6BAI, 5QDE, 5QDG, 5QDF

  • 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. 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 ...

    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: 

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1 A321Homo sapiensMutation(s): 2 
Gene Names: PTPN1, PTP1B
EC: 3.1.3.48
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
NIH Common Fund Data Resources
PHAROS:  P18031
GTEx:  ENSG00000196396
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AWG
Query on AWG
Download Ideal Coordinates CCD File 
A
~{N}2-(1~{H}-benzimidazol-2-yl)benzene-1,2-diamine
C13 H12 N4
ZZDGNBWCSPZNRU-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.786α = 90
b = 89.786β = 90
c = 106.377γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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