2OYF | pdb_00002oyf

Crystal Structure of the complex of phospholipase A2 with indole acetic acid at 1.2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OYF/pdb

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


• Deposited: 2007-02-22 Released: 2007-03-20 
• Deposition Author(s): Kumar, S., Hariprasad, G., Singh, N., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.208 (Depositor) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the complex of phospholipase A2 with indole acetic acid at 1.2 A resolution

Kumar, S., Hariprasad, G., Singh, N., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., 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: 14.35 kDa 
• Atom Count: 1,211 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IAC	G [auth A]	1H-INDOL-3-YLACETIC ACID C10 H9 N O2 SEOVTRFCIGRIMH-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	H [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.208 (Depositor) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.31	α = 90
b = 52.31	β = 90
c = 47.835	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Kumar, S., Hariprasad, G., Singh, N., Sharma, S., Kaur, P., Perbandt, M., Betzel, C., Singh, T.P.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary