3NJU | pdb_00003nju

Crystal structure of the complex of group I phospholipase A2 with 4-Methoxy-benzoicacid at 1.4A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NJU/pdb

• Classification: HYDROLASE
• Organism(s): Naja sagittifera
• Mutation(s): No 


• Deposited: 2010-06-18 Released: 2010-07-14 
• Deposition Author(s): Kaushik, S., Prem Kumar, R., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of group I phospholipase A2 with 4-Methoxy-benzoicacid at 1.4A resolution

Kaushik, S., Prem Kumar, R., 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: 13.32 kDa 
• Atom Count: 1,261 
• Modeled Residue Count: 119 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 isoform 3	A	119	Naja sagittifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P60045 (Naja sagittifera) Explore P60045  Go to UniProtKB:  P60045

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANN	B [auth A]	4-METHOXYBENZOIC ACID C8 H8 O3 ZEYHEAKUIGZSGI-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.074	α = 90
b = 42.074	β = 90
c = 64.253	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Kaushik, S., Prem Kumar, R., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-07-14
  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: 2024-10-30
  Changes: Structure summary