1YXL

Crystal structure of a novel phospholipase A2 from Naja naja sagittifera at 1.5 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1YXL/pdb

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


• Deposited: 2005-02-22 Released: 2005-03-08 
• Deposition Author(s): Singh, R.K., Jabeen, T., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Crystal Structure of a novel phospholipase A2 from Naja naja sagittifera at 1.5 A resolution

Singh, R.K., Jabeen, T., 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: 13.38 kDa 
• Atom Count: 1,065 
• Modelled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.017	α = 90
b = 42.017	β = 90
c = 64.451	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-08 
Deposition Author(s): Singh, R.K., Jabeen, T., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2005-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary