1AOK | pdb_00001aok

VIPOXIN COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1AOK/pdb

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


• Deposited: 1997-07-07 Released: 1998-01-21 
• Deposition Author(s): Perbandt, M., Wilson, J.C., Eschenburg, S., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of vipoxin at 2.0 A: an example of regulation of a toxic function generated by molecular evolution.

Perbandt, M., Wilson, J.C., Eschenburg, S., Mancheva, I., Aleksiev, B., Genov, N., Willingmann, P., Weber, W., Singh, T.P., Betzel, C.

(1997) FEBS Lett 412: 573-577

• PubMed: 9276469 
• DOI: https://doi.org/10.1016/s0014-5793(97)00853-3
• Primary Citation Related Structures: 
  1AOK


• PubMed Abstract: 
  

  Vipoxin is the main toxic component in the venom of the Bulgarian snake Vipera ammodytes meridionalis, the most toxic snake in Europe. Vipoxin is a complex between a toxic phospholipase A2 (PLA2) and a non-toxic protein inhibitor. The structure is of genetic interest due to the high degree of sequence homology (62%) between the two functionally different components. The structure shows that the formation of the complex in vipoxin is significantly different to that seen in many known structures of phospholipases and contradicts the assumptions made in earlier studies. The modulation of PLA2 activity is of great pharmacological interest, and the present structure will be a model for structure-based drug design.

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Organizational Affiliation: 
• Institute of Biochemistry, Free University of Berlin, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.56 kDa 
• Atom Count: 2,204 
• Modeled Residue Count: 244 
• Deposited Residue Count: 244 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VIPOXIN COMPLEX	A	122	Vipera ammodytes meridionalis	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P04084 (Vipera ammodytes meridionalis) Explore P04084  Go to UniProtKB:  P04084

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VIPOXIN COMPLEX	B	122	Vipera ammodytes meridionalis	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.64	α = 90
b = 67.69	β = 90
c = 46.82	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-21 
Deposition Author(s): Perbandt, M., Wilson, J.C., Eschenburg, S., Betzel, C.

Revision History  

• Version 1.0: 1998-01-21
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary