1OYF

Crystal Structure of Russelles viper (Daboia russellii pulchella) phospholipase A2 in a complex with venom 6-methyl heptanol

• PDB DOI: https://doi.org/10.2210/pdb1OYF/pdb

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


• Deposited: 2003-04-04 Released: 2003-05-20 
• Deposition Author(s): Singh, N., Jabeen, T., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Crystal Structure of Russelles viper (Daboia russellii pulchella) phospholipase A2 in a complex with venom 6-methyl heptanol

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.73 kDa 
• Atom Count: 2,081 
• Modelled Residue Count: 242 
• Deposited Residue Count: 242 
• 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
Phospholipase A2	B	121	Daboia russelii pulchella	Mutation(s): 0  EC: 3.1.1.4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MHN	D [auth A], F [auth B]	6-METHYLHEPTAN-1-OL C8 H18 O BWDBEAQIHAEVLV-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.866	α = 90
b = 69.071	β = 90
c = 75.646	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-20 
Deposition Author(s): Singh, N., Jabeen, T., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2003-05-20
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description