3JQL

Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb3JQL/pdb

• Classification: HYDROLASE
• Organism(s): Naja sagittifera, Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2009-09-07 Released: 2009-09-29 
• Deposition Author(s): Mirza, Z., Vikram, G., Singh, N., Sinha, M., Sharma, S., Srinivasan, A., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.193 
• R-Value Work: 0.181 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution

Mirza, Z., Vikram, G., Singh, N., Sinha, M., 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: 13.89 kDa 
• Atom Count: 1,110 
• Modelled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acidic phospholipase A2 3 (Fragment)	A	119	Naja sagittifera	Mutation(s): 0
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	6	N/A	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  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: 1.20 Å
• R-Value Free: 0.193 
• R-Value Work: 0.181 
• R-Value Observed: 0.187 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.023	α = 90
b = 42.023	β = 90
c = 64.146	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., 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, Source and taxonomy, Structure summary