4X94

Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (hexagonal form)

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2014-12-11 Released: 2015-03-11 
  • Deposition Author(s): Glukhova, A., Tesmer, J.J.G.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group XV phospholipase A2380Homo sapiensMutation(s): 0 
Gene Names: PLA2G15, LYPLA3, UNQ341/PRO540
EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCC3 (Homo sapiens)
Explore Q8NCC3 
Go to UniProtKB:  Q8NCC3
PHAROS:  Q8NCC3
GTEx:  ENSG00000103066 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NCC3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
F [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.978α = 90
b = 95.978β = 90
c = 207.943γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
Aimlessdata scaling
Cootmodel building
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL086865

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary