1SKG

Structure-based rational drug design: Crystal structure of the complex formed between Phospholipase A2 and a pentapeptide Val-Ala-Phe-Arg-Ser

• PDB DOI: https://doi.org/10.2210/pdb1SKG/pdb

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


• Deposited: 2004-03-04 Released: 2004-04-27 
• Deposition Author(s): Ethayathulla, A.S., Singh, N., Sharma, S., Makker, J., Dey, S., Perbandt, M., Betzel, C., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.183 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Starting Model: experimental

Literature

Structure-based rational drug design: Crystal structure of the complex formed between Phospholipase A2 and a pentapeptide Val-Ala-Phe-Arg-Ser

Ethayathulla, A.S., Singh, N., Sharma, S., Makker, J., Dey, S., Perbandt, M., Betzel, C., 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: 14.66 kDa 
• Atom Count: 1,258 
• Modelled Residue Count: 126 
• Deposited Residue Count: 126 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VAFRS	B	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MOH	G [auth A], H [auth A]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.183 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.35	α = 90
b = 52.35	β = 90
c = 47.828	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	model building
SHELXL-97	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-27 
Deposition Author(s): Ethayathulla, A.S., Singh, N., Sharma, S., Makker, J., Dey, S., Perbandt, M., Betzel, C., Singh, T.P.

Revision History  

• Version 1.0: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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