1Y4L

Crystal structure of Bothrops asper myotoxin II complexed with the anti-trypanosomal drug suramin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibition of Myotoxic Activity of Bothrops asper Myotoxin II by the Anti-trypanosomal Drug Suramin.

Murakami, M.T.Arruda, E.Z.Melo, P.A.Martinez, A.B.Calil-Elias, S.Tomaz, M.A.Lomonte, B.Gutierrez, J.M.Arni, R.K.

(2005) J Mol Biol 350: 416-426

  • DOI: 10.1016/j.jmb.2005.04.072
  • Primary Citation of Related Structures:  
    1Y4L

  • PubMed Abstract: 
  • Suramin, a synthetic polysulfonated compound, developed initially for the treatment of African trypanosomiasis and onchocerciasis, is currently used for the treatment of several medically relevant disorders. Suramin, heparin, and other polyanions inh ...

    Suramin, a synthetic polysulfonated compound, developed initially for the treatment of African trypanosomiasis and onchocerciasis, is currently used for the treatment of several medically relevant disorders. Suramin, heparin, and other polyanions inhibit the myotoxic activity of Lys49 phospholipase A2 analogues both in vitro and in vivo, and are thus of potential importance as therapeutic agents in the treatment of viperid snake bites. Due to its conformational flexibility around the single bonds that link the central phenyl rings to the secondary amide backbone, the symmetrical suramin molecule binds by an induced-fit mechanism complementing the hydrophobic surfaces of the dimer and adopts a novel conformation that lacks C2 symmetry in the dimeric crystal structure of the suramin-Bothrops asper myotoxin II complex. The simultaneous binding of suramin at the surfaces of the two monomers partially restricts access to the nominal active sites and significantly changes the overall charge of the interfacial recognition face of the protein, resulting in the inhibition of myotoxicity.


    Organizational Affiliation

    Departament of Physics, IBILCE/UNESP, São José do Rio Preto, SP, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase A2 homolog 2AB121Bothrops asperMutation(s): 0 
EC: 3.1.1.4
Find proteins for P24605 (Bothrops asper)
Explore P24605 
Go to UniProtKB:  P24605
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SVR
Query on SVR

Download CCD File 
B
8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID
C51 H40 N6 O23 S6
FIAFUQMPZJWCLV-UHFFFAOYSA-N
 Ligand Interaction
P33
Query on P33

Download CCD File 
A, B
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download CCD File 
A, B
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.199α = 90
b = 64.037β = 90
c = 85.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description