1KQU | pdb_00001kqu

Human phospholipase A2 complexed with a substrate anologue

• PDB DOI: https://doi.org/10.2210/pdb1KQU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-01-07 Released: 2003-11-11 
• Deposition Author(s): Tyndall, J.D., Martin, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

D-Tyrosine as a chiral precusor to potent inhibitors of human nonpancreatic secretory phospholipase A2 (IIa) with antiinflammatory activity.

Hansford, K.A., Reid, R.C., Clark, C.I., Tyndall, J.D., Whitehouse, M.W., Guthrie, T., McGeary, R.P., Schafer, K., Martin, J.L., Fairlie, D.P.

(2003) Chembiochem 4: 181-185

• PubMed: 12616631 
• DOI: https://doi.org/10.1002/cbic.200390029
• Primary Citation Related Structures: 
  1J1A, 1KQU


• PubMed Abstract: 
  

  Few reported inhibitors of secretory phospholipase A(2) enzymes truly inhibit the IIa human isoform (hnpsPLA(2)-IIa) noncovalently at submicromolar concentrations. Herein, the simple chiral precursor D-tyrosine was derivatised to give a series of potent new inhibitors of hnpsPLA(2)-IIa. A 2.2-A crystal structure shows an inhibitor bound in the active site of the enzyme, chelated to a Ca(2+) ion through carboxylate and amide oxygen atoms, H-bonded through an amide NH group to His48, with multiple hydrophobic contacts and a T-shaped aromatic-group-His6 interaction. Antiinflammatory activity is also demonstrated for two compounds administered orally to rats.

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Organizational Affiliation: 
• Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland Brisbane, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.42 kDa 
• Atom Count: 1,065 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2, membrane associated	A	124	Homo sapiens	Mutation(s): 0  EC: 3.1.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P14555 (Homo sapiens) Explore P14555  Go to UniProtKB:  P14555
PHAROS:  P14555 GTEx:  ENSG00000188257

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR4	D [auth A]	6-PHENYL-4(R)-(7-PHENYL-HEPTANOYLAMINO)-HEXANOIC ACID C25 H33 N O3 SMNHQYPORNSAQH-HSZRJFAPSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.55	α = 90
b = 76.55	β = 90
c = 93.46	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): Tyndall, J.D., Martin, J.L.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary