3CBI

Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CBI/pdb

• Classification: HYDROLASE
• Organism(s): Daboia russelii pulchella
• Mutation(s): No 


• Deposited: 2008-02-22 Released: 2008-03-11 
• Deposition Author(s): Kumar, S., Vikram, G., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.250 
• R-Value Work: 0.228 

Literature

Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution

Kumar, S., Vikram, G., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.32 kDa 
• Atom Count: 3,904 
• Modelled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 VRV-PL-VIIIa	A, B, C, D	121	Daboia russelii pulchella	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P59071 (Daboia russelii) Explore P59071  Go to UniProtKB:  P59071

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AJM	E [auth A], G [auth B], I [auth C], K [auth D]	AJMALINE C18 H22 N2 O2 CFEPCEVMXPTZPJ-OGDRVKPDSA-N
ANN	F [auth A], H [auth B], J [auth C], L [auth D]	4-METHOXYBENZOIC ACID C8 H8 O3 ZEYHEAKUIGZSGI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.250 
• R-Value Work: 0.228 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.799	α = 90
b = 108.799	β = 90
c = 43.339	γ = 120

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: 2008-03-11 
Deposition Author(s): Kumar, S., Vikram, G., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description