4GLD

Crystal Structure of the complex of type II phospholipase A2 with a designed peptide inhibitor Phe - Leu - Ala - Tyr - Lys at 1.69 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4GLD/pdb

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


• Deposited: 2012-08-14 Released: 2012-08-29 
• Deposition Author(s): Shukla, P.K., Sinha, M., Dey, S., Kaur, P., Sharma, S., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.199 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Crystal Structure of the complex of type II phospholipase A2 with a designed peptide inhibitor Phe - Leu - Ala - Tyr - Lys at 1.69 A resolution

Shukla, P.K., Sinha, M., Dey, S., Kaur, P., Sharma, S., 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: 14.52 kDa 
• Atom Count: 1,152 
• 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 VRV-PL-VIIIa	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
FLAYK	B	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.199 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.777	α = 90
b = 51.777	β = 90
c = 47.484	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Shukla, P.K., Sinha, M., Dey, S., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description