3FO7 | pdb_00003fo7

Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site

• PDB DOI: https://doi.org/10.2210/pdb3FO7/pdb
• Entry: 3FO7 supersedes: 2DV8

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


• Deposited: 2008-12-29 Released: 2009-01-20 
• Deposition Author(s): Singh, N., Prem Kumar, R., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.202 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site

Singh, N., Prem Kumar, R., 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)

Macromolecule Content 

• Total Structure Weight: 14.37 kDa 
• Atom Count: 1,267 
• 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
IMN	F [auth A]	INDOMETHACIN C19 H16 Cl N O4 CGIGDMFJXJATDK-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.202 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.66	α = 90
b = 51.66	β = 90
c = 48.003	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Singh, N., Prem Kumar, R., Sharma, S., Kaur, P., Singh, T.P.
• This entry supersedes: 2DV8

Revision History  

• Version 1.0: 2009-01-20
  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
• Version 1.3: 2024-11-20
  Changes: Structure summary