3L30 | pdb_00003l30

Crystal structure of porcine pancreatic phospholipase A2 complexed with dihydroxyberberine

• PDB DOI: https://doi.org/10.2210/pdb3L30/pdb

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


• Deposited: 2009-12-16 Released: 2010-01-26 
• Deposition Author(s): Naveen, C., Prasanth, G.K., Abhilash, J., Pradeep, M., Ponnuraj, K., Sadasivan, C., Haridas, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.240 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of porcine pancreatic phospholipase A2 complexed with dihydroxyberberine

Naveen, C., Prasanth, G.K., Abhilash, J., Pradeep, M., Ponnuraj, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,105 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DBW	E [auth A]	4,14-dihydro-8H-[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinoline-9,10-diol C18 H15 N O4 LCTIMSLMTIKISI-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.240 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.88	α = 90
b = 68.88	β = 90
c = 70.16	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AUTOMAR	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Naveen, C., Prasanth, G.K., Abhilash, J., Pradeep, M., Ponnuraj, K., Sadasivan, C., Haridas, M.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary