3Q4Y | pdb_00003q4y

Crystal structure of group I phospholipase A2 at 2.3 A resolution in 40% ethanol revealed the critical elements of hydrophobicity of the substrate-binding site

• PDB DOI: https://doi.org/10.2210/pdb3Q4Y/pdb

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


• Deposited: 2010-12-26 Released: 2011-01-26 
• Deposition Author(s): Shukla, P.K., Kaushik, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of group I phospholipase A2 at 2.3 A resolution in 40% ethanol revealed the critical elements of hydrophobicity of the substrate-binding site

Shukla, P.K., Kaushik, S., 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: 13.21 kDa 
• Atom Count: 997 
• 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
EOH	C [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.153	α = 90
b = 42.153	β = 90
c = 65	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: 2011-01-26 
Deposition Author(s): Shukla, P.K., Kaushik, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-07-18
  Changes: Data collection, Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary