4CML

Crystal Structure of INPP5B in complex with Phosphatidylinositol 3,4- bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases.

Tresaugues, L.Silvander, C.Flodin, S.Welin, M.Nyman, T.Graslund, S.Hammarstrom, M.Berglund, H.Nordlund, P.

(2014) Structure 22: 744

  • DOI: https://doi.org/10.1016/j.str.2014.01.013
  • Primary Citation of Related Structures:  
    3MTC, 3N9V, 3NR8, 4CML, 4CMN

  • PubMed Abstract: 

    SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phophatases is still poorly understood. We determined the crystal structures of human SHIP2, OCRL, and INPP5B, the latter in complex with phosphoinositide substrate analogs, which revealed a membrane interaction patch likely to assist in sequestering substrates from the lipid bilayer. Residues recognizing the 1-phosphate of the substrates are highly conserved among human family members, suggesting similar substrate binding modes. However, 3- and 4-phosphate recognition varies and determines individual substrate specificity profiles. The high conservation of the environment of the scissile 5-phosphate suggests a common reaction geometry for all members of the human 5-phosphatase family.


  • Organizational Affiliation

    Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2313Homo sapiensMutation(s): 0 
EC: 3.1.3.36
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P32019 (Homo sapiens)
Explore P32019 
Go to UniProtKB:  P32019
PHAROS:  P32019
GTEx:  ENSG00000204084 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32019
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
52N
Query on 52N

Download Ideal Coordinates CCD File 
B [auth A]1,2-dioctanoyl phosphatidyl epi-inositol (3,4)-bisphosphate
C25 H49 O19 P3
XLNCEHRXXWQMPK-KWIFDMFUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.661α = 90
b = 133.661β = 90
c = 133.661γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description