5WZM

Crystal structure of human secreted phospholipase A2 group IIE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2 group IIE

Hou, S.Xu, T.Xu, J.Qu, L.Xu, Y.Chen, L.Liu, J.

(2017) Sci Rep 7: 10815-10815

  • DOI: 10.1038/s41598-017-11219-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Secreted phospholipases A2s (sPLA2s) are involved in various pathological conditions such as rheumatoid arthritis and cardiovascular disease. Many inhibitors were developed and studied in clinical trials, but none have reached the market yet. This fa ...

    Secreted phospholipases A2s (sPLA2s) are involved in various pathological conditions such as rheumatoid arthritis and cardiovascular disease. Many inhibitors were developed and studied in clinical trials, but none have reached the market yet. This failure may be attributed to the lack of subtype selectivity for these inhibitors. Therefore, more structural information for subtype sPLA2 is needed to guide the selective inhibitor development. In this study, the crystal structure of human sPLA2 Group IIE (hGIIE), coupled with mutagenesis experiments, proved that the flexible second calcium binding site and residue Asn21 in hGIIE are essential to its enzymatic activity. Five inhibitor bound hGIIE complex structures revealed the key residues (Asn21 and Gly6) of hGIIE that are responsible for interacting with inhibitors, and illustrated the difference in the inhibitor binding pocket with other sPLA2s. This will facilitate the structure-based design of sPLA2's selective inhibitors.


    Organizational Affiliation

    State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Group IIE secretory phospholipase A2
A
121Homo sapiensMutation(s): 0 
Gene Names: PLA2G2E
EC: 3.1.1.4
Find proteins for Q9NZK7 (Homo sapiens)
Go to Gene View: PLA2G2E
Go to UniProtKB:  Q9NZK7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • Space Group: P 21 2 2
Unit Cell:
Length (Å)Angle (°)
a = 48.510α = 90.00
b = 60.460β = 90.00
c = 63.590γ = 90.00
Software Package:
Software NamePurpose
MOLREPmodel building
MOLREPphasing
REFMACrefinement
Aimlessdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release