4DBK

Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine

• PDB DOI: https://doi.org/10.2210/pdb4DBK/pdb
• Entry: 4DBK supersedes: 3L69, 3TT5

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


• Deposited: 2012-01-16 Released: 2012-01-25 
• Deposition Author(s): Naveen, C.D., Abhilash, J., Prasanth, G.K., Sadasivan, C., Haridas, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine

Naveen, C.D., Abhilash, J., Prasanth, G.K., Sadasivan, C., Haridas, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,104 
• Modelled 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
BER	D [auth A]	BERBERINE C20 H18 N O4 YBHILYKTIRIUTE-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: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.6	α = 90
b = 68.6	β = 90
c = 70.08	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Naveen, C.D., Abhilash, J., Prasanth, G.K., Sadasivan, C., Haridas, M.
• This entry supersedes: 3L69, 3TT5

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary