2QU9 | pdb_00002qu9

Crystal structure of the complex of group II phospholipase A2 with Eugenol

• PDB DOI: https://doi.org/10.2210/pdb2QU9/pdb

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


• Deposited: 2007-08-04 Released: 2007-08-14 
• Deposition Author(s): Kumar, S., Vikram, G., Singh, N., Sinha, M., Sharma, S., Kaur, P., Srinivasan, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.217 (Depositor) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of group II phospholipase A2 with Eugenol

Kumar, S., Vikram, G., Singh, N., Sinha, M., Sharma, S., Kaur, P., Srinivasan, A., 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)

Macromolecule Content 

• Total Structure Weight: 13.89 kDa 
• Atom Count: 1,033 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 VRV-PL-VIIIa	A	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
EUG	C [auth A]	2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol C10 H12 O2 BJIOGJUNALELMI-ONEGZZNKSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.217 (Depositor) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.795	α = 90
b = 52.795	β = 90
c = 48.397	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Kumar, S., Vikram, G., Singh, N., Sinha, M., Sharma, S., Kaur, P., Srinivasan, A., Singh, T.P.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary