1SQZ

Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between Group II Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution

• PDB DOI: https://doi.org/10.2210/pdb1SQZ/pdb

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


• Deposited: 2004-03-22 Released: 2004-04-13 
• Deposition Author(s): Singh, N., Prem Kumar, R., Somvanshi, R.K., Bilgrami, S., Ethayathulla, A.S., Sharma, S., Dey, S., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.217 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between GroupII Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution

Singh, N., Prem Kumar, R., Somvanshi, R.K., Bilgrami, S., Ethayathulla, A.S., Sharma, S., Dey, 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: 1,300 
• 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 russelii	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
synthetic peptide	B	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000335	B	DEHYDRO-ILE-ALA-ARG-SER	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.217 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.549	α = 90
b = 52.549	β = 90
c = 47.833	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-13 
Deposition Author(s): Singh, N., Prem Kumar, R., Somvanshi, R.K., Bilgrami, S., Ethayathulla, A.S., Sharma, S., Dey, S., Singh, T.P.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description