1V6P

Crystal structure of Cobrotoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing

Lou, X.Liu, Q.Tu, X.Wang, J.Teng, M.Niu, L.Schuller, D.J.Huang, Q.Hao, Q.

(2004) J.Biol.Chem. 279: 39094-39104

  • DOI: 10.1074/jbc.M403863200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By using single wavelength anomalous diffraction phasing based on the anomalous signal from copper atoms, the crystal structure of atratoxin was determined at the resolution of 1.5 A and was refined to an ultrahigh resolution of 0.87 A. The ultrahigh ...

    By using single wavelength anomalous diffraction phasing based on the anomalous signal from copper atoms, the crystal structure of atratoxin was determined at the resolution of 1.5 A and was refined to an ultrahigh resolution of 0.87 A. The ultrahigh resolution electron density maps allowed the modeling of 38 amino acid residues in alternate conformations and the location of 322 of 870 possible hydrogen atoms. To get accurate information at the atomic level, atratoxin-b (an analog of atratoxin with reduced toxicity) was also refined to an atomic resolution of 0.92 A. By the sequence and structural comparison of these two atratoxins, Arg(33) and Arg(36) were identified to be critical to their varied toxicity. The effect of copper ions on the distribution of hydrogen atoms in atratoxin was discussed, and the interactions between copper ions and protein residues were analyzed based on a statistical method, revealing a novel pentahedral copper-binding motif.


    Organizational Affiliation

    Key Laboratory of Structural Biology, Chinese Academy of Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cobrotoxin
A, B
62Naja atraMutation(s): 0 
Find proteins for P60770 (Naja atra)
Go to UniProtKB:  P60770
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

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A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

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A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.119 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 46.808α = 90.00
b = 47.287β = 90.00
c = 90.018γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SHELXmodel building
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance