1Y38 | pdb_00001y38

Crystal structure of the complex formed between phospholipase A2 dimer and glycerophosphate at 2.4 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1Y38/pdb

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


• Deposited: 2004-11-24 Released: 2005-05-03 
• Deposition Author(s): Singh, N., Jabeen, T., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of the complex formed between phospholipase A2 dimer and glycerophosphate at 2.4 A resolution

Singh, N., Jabeen, T., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.87 kDa 
• Atom Count: 2,109 
• Modeled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 VRV-PL-VIIIa	A, B	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3P	E [auth A], F [auth B]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N
PGE	G [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.866	α = 90
b = 69.071	β = 90
c = 75.646	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-03 
Deposition Author(s): Singh, N., Jabeen, T., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2005-05-03
  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: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary