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 

Starting Model: experimental
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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
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  • 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

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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