4WRI

Crystal structure of okadaic acid binding protein 2.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Okadaic Acid Binding Protein 2.1: A Sponge Protein Implicated in Cytotoxin Accumulation

Ehara, H.Makino, M.Kodama, K.Konoki, K.Ito, T.Sekine, S.Fukuzawa, S.Yokoyama, S.Tachibana, K.

(2015) Chembiochem 16: 1435-1439

  • DOI: https://doi.org/10.1002/cbic.201500141
  • Primary Citation of Related Structures:  
    4WRI

  • PubMed Abstract: 

    Okadaic acid (OA) is a marine polyether cytotoxin that was first isolated from the marine sponge Halichondria okadai. OA is a potent inhibitor of protein serine/threonine phosphatases (PP) 1 and 2A, and the structural basis of phosphatase inhibition has been well investigated. However, the role and mechanism of OA retention in the marine sponge have remained elusive. We have solved the crystal structure of okadaic acid binding protein 2.1 (OABP2.1) isolated from H. okadai; it has strong affinity for OA and limited sequence homology to other proteins. The structure revealed that OABP2.1 consists of two α-helical domains, with the OA molecule deeply buried inside the protein. In addition, the global fold of OABP2.1 was unexpectedly similar to that of aequorin, a jellyfish photoprotein. The presence of structural homologues suggested that, by using similar protein scaffolds, marine invertebrates have developed diverse survival systems adapted to their living environments.


  • Organizational Affiliation

    Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Okadaic acid binding protein 2-alpha192Halichondria okadaiMutation(s): 0 
Gene Names: OABP2AOABP2.1
UniProt
Find proteins for Q2MHR1 (Halichondria okadai)
Explore Q2MHR1 
Go to UniProtKB:  Q2MHR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2MHR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OKA
Query on OKA

Download Ideal Coordinates CCD File 
B [auth A]OKADAIC ACID
C44 H68 O13
QNDVLZJODHBUFM-WFXQOWMNSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.97α = 90
b = 64.62β = 90
c = 145.24γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan21603006

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations, Other, Source and taxonomy, Structure summary