2RD4

Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of phospholipase A2 with pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RD4/pdb

• Classification: HYDROLASE
• Organism(s): Naja sagittifera
• Mutation(s): No 


• Deposited: 2007-09-21 Released: 2007-10-09 
• Deposition Author(s): Mirza, Z., Kaur, A., Singh, N., Sinha, M., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 0.274 
• R-Value Work: 0.251 
• R-Value Observed: 0.258 

Starting Model: experimental

Literature

Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of phospholipase A2 with pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A resolution

Mirza, Z., Kaur, A., Singh, N., Sinha, M., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.19 kDa 
• Atom Count: 1,940 
• Modelled Residue Count: 243 
• Deposited Residue Count: 243 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 isoform 1	A	119	Naja sagittifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P60043 (Naja sagittifera) Explore P60043  Go to UniProtKB:  P60043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 isoform 2	B	119	Naja sagittifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P60044 (Naja sagittifera) Explore P60044  Go to UniProtKB:  P60044

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
pentapeptide inhibitor	C	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 0.274 
• R-Value Work: 0.251 
• R-Value Observed: 0.258 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.54	α = 90
b = 65.54	β = 90
c = 58.551	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Mirza, Z., Kaur, A., Singh, N., Sinha, M., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-31
  Changes: Experimental preparation
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary