4EIX | pdb_00004eix

Structural Studies of the ternary complex of Phaspholipase A2 with nimesulide and indomethacin

• PDB DOI: https://doi.org/10.2210/pdb4EIX/pdb

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


• Deposited: 2012-04-06 Released: 2012-04-25 
• Deposition Author(s): Shukla, P.K., Singh, N., Kumar, S., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.208 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural Studies of the ternary complex of Phaspholipase A2 with nimusulide and indomethacin

Shukla, P.K., Singh, N., Kumar, S., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., 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: 14.34 kDa 
• Atom Count: 1,036 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMN	C [auth A]	INDOMETHACIN C19 H16 Cl N O4 CGIGDMFJXJATDK-UHFFFAOYSA-N
NIM	B [auth A]	4-NITRO-2-PHENOXYMETHANESULFONANILIDE C13 H12 N2 O5 S HYWYRSMBCFDLJT-UHFFFAOYSA-N
CCN	D [auth A]	ACETONITRILE C2 H3 N WEVYAHXRMPXWCK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.208 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.88	α = 90
b = 52.88	β = 90
c = 48.42	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Shukla, P.K., Singh, N., Kumar, S., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary