3JQ5 | pdb_00003jq5

Phospholipase A2 Prevents the Aggregation of Amyloid Beta Peptides: Crystal Structure of the Complex of Phospholipase A2 with Octapeptide Fragment of Amyloid Beta Peptide, Asp-Ala-Glu-Phe-Arg-His-Asp-Ser at 2 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb3JQ5/pdb

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


• Deposited: 2009-09-06 Released: 2009-09-29 
• Deposition Author(s): Mirza, Z., Vikram, G., Singh, N., Sinha, M., Bhushan, A., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.221 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Phospholipase A2 Prevents the Aggregation of Amyloid Beta Peptides: Crystal Structure of the Complex of Phospholipase A2 with Octapeptide Fragment of Amyloid Beta Peptide, Asp-Ala-Glu-Phe-Arg-His-Asp-Ser at 2 A Resolution

Mirza, Z., Vikram, G., Singh, N., Sinha, M., Bhushan, A., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 14.15 kDa 
• Atom Count: 1,077 
• Modeled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid Beta Peptide	B	8	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.221 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.795	α = 90
b = 42.795	β = 90
c = 65.832	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Mirza, Z., Vikram, G., Singh, N., Sinha, M., Bhushan, A., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2009-09-29
  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