3DIH | pdb_00003dih

Crystal structure of ammodytin L

• PDB DOI: https://doi.org/10.2210/pdb3DIH/pdb

• Classification: TOXIN
• Organism(s): Vipera ammodytes ammodytes
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-06-20 Released: 2008-08-05 
• Deposition Author(s): Turk, D., Guncar, G., Krizaj, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Crystal structure of ammodytin L

Turk, D., Guncar, G., Krizaj, I.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.9 kDa 
• Atom Count: 1,067 
• Modeled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 homolog, ammodytin L	A	122	Vipera ammodytes ammodytes	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P17935 (Vipera ammodytes ammodytes) Explore P17935  Go to UniProtKB:  P17935

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.226 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.5	α = 90
b = 120.5	β = 90
c = 63.15	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
MAIN	refinement
MOSFLM	data reduction
rotavata/agrovata	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Turk, D., Guncar, G., Krizaj, I.

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary