1D5R | pdb_00001d5r

Crystal Structure of the PTEN Tumor Suppressor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.276 (Depositor) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association.

Lee, J.O.Yang, H.Georgescu, M.M.Di Cristofano, A.Maehama, T.Shi, Y.Dixon, J.E.Pandolfi, P.Pavletich, N.P.

(1999) Cell 99: 323-334

  • DOI: https://doi.org/10.1016/s0092-8674(00)81663-3
  • Primary Citation Related Structures: 
    1D5R

  • PubMed Abstract: 

    The PTEN tumor suppressor is mutated in diverse human cancers and in hereditary cancer predisposition syndromes. PTEN is a phosphatase that can act on both polypeptide and phosphoinositide substrates in vitro. The PTEN structure reveals a phosphatase domain that is similar to protein phosphatases but has an enlarged active site important for the accommodation of the phosphoinositide substrate. The structure also reveals that PTEN has a C2 domain. The PTEN C2 domain binds phospholipid membranes in vitro, and mutation of basic residues that could mediate this reduces PTEN's membrane affinity and its ability to suppress the growth of glioblastoma tumor cells. The phosphatase and C2 domains associate across an extensive interface, suggesting that the C2 domain may serve to productively position the catalytic domain on the membrane.


  • Organizational Affiliation
    • Cellular Biochemistry and Biophysics Program, Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 38.65 kDa 
  • Atom Count: 2,968 
  • Modeled Residue Count: 307 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHOINOSITIDE PHOSPHATASE PTEN324Homo sapiensMutation(s): 0 
EC: 3.1.3.48 (PDB Primary Data), 3.1.3.67 (UniProt), 3.1.3 (UniProt), 3.1.3.16 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60484 (Homo sapiens)
Explore P60484 
Go to UniProtKB:  P60484
PHAROS:  P60484
GTEx:  ENSG00000171862 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60484
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TLA

Query on TLA



Download:Ideal Coordinates CCD File
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.276 (Depositor) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.14α = 90
b = 113.14β = 90
c = 58.55γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-04
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-02-24
    Changes: Structure summary
  • Version 1.4: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.5: 2024-02-07
    Changes: Data collection, Database references, Derived calculations