4G5I | pdb_00004g5i

Crystal Structure of Porcine pancreatic PlA2 in complex with DBP

• PDB DOI: https://doi.org/10.2210/pdb4G5I/pdb

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


• Deposited: 2012-07-18 Released: 2012-11-07 
• Deposition Author(s): Prasanth, G.K., Naveen, C.D., Mandal, P.K., Karthe, P., Haridas, M., Sadasivan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal Structure of Porcine pancreatic PlA2 in complex with DBP

Prasanth, G.K., Naveen, C.D., Mandal, P.K., Karthe, P., Haridas, M., Sadasivan, C.

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: 14.44 kDa 
• Atom Count: 1,078 
• 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
DB7	F [auth A]	dibutyl benzene-1,2-dicarboxylate C16 H22 O4 DOIRQSBPFJWKBE-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.243 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.86	α = 90
b = 68.86	β = 90
c = 70.18	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Prasanth, G.K., Naveen, C.D., Mandal, P.K., Karthe, P., Haridas, M., Sadasivan, C.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary