2OTH | pdb_00002oth

Crystal structure of a ternary complex of phospholipase A2 with indomethacin and nimesulide at 2.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OTH/pdb

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


• Deposited: 2007-02-08 Released: 2007-02-27 
• Deposition Author(s): Kumar, S., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a ternary complex of phospholipase A2 with indomethacin and nimesulide at 2.9 A resolution

Kumar, S., 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.

Macromolecule Content 

• Total Structure Weight: 14.34 kDa 
• Atom Count: 1,041 
• 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:  0.232 (Depositor) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.189 (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
CNS	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Kumar, S., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary