Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.75 kDa 
• Atom Count: 2247 
• Modelled Residue Count: 244 
• Deposited Residue Count: 244 
• Unique protein chains: 2

1JLT

Vipoxin Complex

• PDB DOI: 10.2210/pdb1JLT/pdb

• Classification: HYDROLASE
• Organism(s): Vipera ammodytes ammodytes
• Mutation(s): No 


• Deposited: 2001-07-16 Released: 2001-10-31 
• Deposition Author(s): Banumathi, S., Rajashankar, K.R., Notzel, C., Aleksiev, B., Singh, T.P., Genov, N., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.195 
• R-Value Work: 0.182 

Literature

Structure of the neurotoxic complex vipoxin at 1.4 A resolution.

Banumathi, S., Rajashankar, K.R., Notzel, C., Aleksiev, B., Singh, T.P., Genov, N., Betzel, C.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1552-1559

• PubMed: 11679719 
• DOI: 10.1107/s0907444901013543
• Primary Citation of Related Structures:  
  1JLT


• PubMed Abstract: 
  

Vipoxin is a neurotoxic postsynaptic heterodimeric complex from the venom of Vipera ammodytes meridionalis, the most toxic snake in Europe. It consists of a basic and highly toxic phospholipase A(2) and an acidic non-toxic protein inhibitor. The two polypeptide chains have the same chain length and share 62% amino-acid identity. Vipoxin is a unique example of evolution of the catalytic and toxic phospholipase A(2) functions into inhibitory and non-toxic functions. The crystal structure of the complex has been determined by the molecular-replacement method and refined to 1.4 A resolution to an R factor of 18.2%. The complex formation decreases the accessible surface area of the two subunits by approximately 1480 A(2), which results in a reduction of toxicity and catalytic activity. The catalytic and substrate-binding sites of the vipoxin phospholipase A(2) are identical or similar to those of other group I/II enzymes. Two 2-methyl-2,4-pentanediol molecules are present in the hydrophobic channel close to the active site. The two subunits lack calcium ions. The negatively charged Asp49 of the phospholipase A(2), which participates in the Ca(2+)-binding sites of other snake-venom phospholipase A(2)s, is neutralized by the side chain of Lys69 from the inhibitor. Attempts have been made to identify the toxicity region and to explain the reduced catalytic activity and toxicity of the phospholipase A(2) subunit.

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Organizational Affiliation: 

Institute of Medical Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2 INHIBITOR	A	122	Vipera ammodytes ammodytes	Mutation(s): 0
UniProt
Find proteins for P04084 (Vipera ammodytes meridionalis) Explore P04084  Go to UniProtKB:  P04084

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2	B	122	Vipera ammodytes ammodytes	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P14420 (Vipera ammodytes meridionalis) Explore P14420  Go to UniProtKB:  P14420

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD	C [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.195 
• R-Value Work: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.049	α = 90
b = 54.708	β = 90
c = 104.76	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-16 
• Released Date: 2001-10-31 
Deposition Author(s): Banumathi, S., Rajashankar, K.R., Notzel, C., Aleksiev, B., Singh, T.P., Genov, N., Betzel, C.

Revision History  

• Version 1.0: 2001-10-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2018-01-31
  Changes: Experimental preparation