1SUG

1.95 A structure of apo protein tyrosine phosphatase 1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B.

Pedersen, A.K.Peters G, G.H.Moller, K.B.Iversen, L.F.Kastrup, J.S.

(2004) Acta Crystallogr.,Sect.D 60: 1527-1534

  • DOI: 10.1107/S0907444904015094
  • Also Cited By: 6B90

  • PubMed Abstract: 
  • Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural in ...

    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 A apo PTP1B structure has been obtained, showing four highly coordinated water molecules in the active-site pocket of the enzyme; hence, the active site is highly solvated in the apo state. Three of the water molecules are located at positions that approximately correspond to the positions of the phosphate O atoms of the natural substrate phosphotyrosine and form a similar network of hydrogen bonds. The active-site WPD-loop was found to be in the closed conformation, in contrast to previous observations of wild-type PTPs in the apo state, in which the WPD-loop is open. The closed conformation is stabilized by a network of hydrogen bonds. These results provide new insights into and understanding of the active site of PTP1B and form a novel basis for structure-based inhibitor design.


    Related Citations: 
    • Affinity purification of recombinant protein-tyrosine phosphatase 1B using a highly selective inhibitor
      Pedersen, A.K.,Branner, S.,Mortensen, S.B.,Andersen, H.S.,Klausen, K.M.,Moller, K.B.,Moller, N.P.,Iversen, L.F.
      (2004) J.Chromatogr.,B 799: 1
    • Crystal structure of human protein tyrosine phosphatase 1B
      Barford, D.,Flint, A.J.,Tonks, N.K.
      (1994) Science 263: 1397


    Organizational Affiliation

    Protein Science, Novo Nordisk, DK-2880 Bagsvaerd, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine phosphatase, non-receptor type 1
A
321Homo sapiensMutation(s): 0 
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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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: 1.95 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.188 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.118α = 90.00
b = 88.118β = 90.00
c = 103.900γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance