3O4M | pdb_00003o4m

Crystal structure of porcine pancreatic phospholipase A2 in complex with 1,2-dihydroxybenzene

• PDB DOI: https://doi.org/10.2210/pdb3O4M/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2010-07-27 Released: 2010-08-25 
• Deposition Author(s): Dileep, K.V., Tintu, I., Karthe, P., Mandal, P.K., Haridas, M., Sadasivan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.223 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Binding to PLA(2) may contribute to the anti-inflammatory activity of catechol

Dileep, K.V., Tintu, I., Mandal, P.K., Karthe, P., Haridas, M., Sadasivan, C.

(2011) Chem Biol Drug Des 

• PubMed: 21995306 
• DOI: https://doi.org/10.1111/j.1747-0285.2011.01258.x
• Primary Citation Related Structures: 
  3O4M


• PubMed Abstract: 
  

  Inhibiting PLA(2) activity should, in theory, be an effective approach to control the inflammation. Several naturally occurring polyphenolic compounds have been reported as inhibitors of PLA(2) . Among the naturally occurring polyphenols, catechol (1,2-dihydroxybenzene) possesses anti-inflammatory activity. Catechol can inhibit cyclooxygenase and lipo-oxygenase. By means of enzyme kinetic study, it was revealed that catechol can inhibit PLA(2) also. Crystal structure showed that catechol binds to PLA(2) at the opening of the active site cleft. This might stop the entry of substrate into the active site. Hence, catechol can be used as a lead compound for the development of novel anti-inflammatory drugs with PLA(2) as the target.

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Organizational Affiliation: 
• Department of Biotechnology and Microbiology, Kannur University, Thalassery Campus, Palayad, Kerala, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.2 kDa 
• Atom Count: 1,037 
• 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, major isoenzyme	A	124	Sus scrofa	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P00592 (Sus scrofa) Explore P00592  Go to UniProtKB:  P00592

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAQ	D [auth A]	CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.223 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.24	α = 90
b = 69.24	β = 90
c = 69.67	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
Auto	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
Auto	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Dileep, K.V., Tintu, I., Karthe, P., Mandal, P.K., Haridas, M., Sadasivan, C.

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-23
  Changes: Database references, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary