1ZYX | pdb_00001zyx

Crystal structure of the complex of a group IIA phospholipase A2 with a synthetic anti-inflammatory agent licofelone at 1.9A resolution

• PDB DOI: https://doi.org/10.2210/pdb1ZYX/pdb

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


• Deposited: 2005-06-13 Released: 2005-06-28 
• Deposition Author(s): Singh, N., Jabeen, T., Sharma, S., Bhushan, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.219 (Depositor) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of the complex of a group IIA phospholipase A2 with a synthetic anti-inflammatory agent licofelone at 1.9A resolution

Singh, N., Jabeen, T., Sharma, S., Bhushan, A., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.2 kDa 
• Atom Count: 1,142 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LCF	D [auth A]	[6-(4-CHLOROPHENYL)-2,2-DIMETHYL-7-PHENYL-2,3-DIHYDRO-1H-PYRROLIZIN-5-YL]ACETIC ACID C23 H22 Cl N O2 UAWXGRJVZSAUSZ-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.219 (Depositor) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.44	α = 90
b = 53.44	β = 90
c = 48.57	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
AUTOMAR	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Singh, N., Jabeen, T., Sharma, S., Bhushan, A., Singh, T.P.

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary