1QIV

CALMODULIN COMPLEXED WITH N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(3,4-BIS-BUTOXYPHENYL)-ETHYL]-PROPYLENEDIAMINE (DPD), 1:2 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies

Harmat, V.Bocskei, Z.S.Naray-Szabo, G.Bata, I.Csutor, A.S.Hermecz, I.Aranyi, P.Szabo, B.Liliom, K.Vertessy, B.G.Ovadi, J.

(2000) J Mol Biol 297: 747

  • DOI: https://doi.org/10.1006/jmbi.2000.3607
  • Primary Citation of Related Structures:  
    1QIV, 1QIW

  • PubMed Abstract: 

    An arylalkylamine-type calmodulin antagonist, N-(3, 3-diphenylpropyl)-N'-[1-R-(3, 4-bis-butoxyphenyl)ethyl]-propylene-diamine (AAA) is presented and its complexes with calmodulin are characterized in solution and in the crystal. Near-UV circular dichroism spectra show that AAA binds to calmodulin with 2:1 stoichiometry in a Ca(2+)-dependent manner. The crystal structure with 2:1 stoichiometry is determined to 2.64 A resolution. The binding of AAA causes domain closure of calmodulin similar to that obtained with trifluoperazine. Solution and crystal data indicate that each of the two AAA molecules anchors in the hydrophobic pockets of calmodulin, overlapping with two trifluoperazine sites, i.e. at a hydrophobic pocket and an interdomain site. The two AAA molecules also interact with each other by hydrophobic forces. A competition enzymatic assay has revealed that AAA inhibits calmodulin-activated phosphodiesterase activity at two orders of magnitude lower concentration than trifluoperazine. The apparent dissociation constant of AAA to calmodulin is 18 nM, which is commensurable with that of target peptides. On the basis of the crystal structure, we propose that the high-affinity binding is mainly due to a favorable entropy term, as the AAA molecule makes multiple contacts in its complex with calmodulin.


  • Organizational Affiliation

    Department of Theoretical Chemistry, Loránd Eötvös University, Budapest 112, H-1518, Hungary. harmatv@ludens.elte.hu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CALMODULIN148Bos taurusMutation(s): 0 
UniProt
Find proteins for P62157 (Bos taurus)
Explore P62157 
Go to UniProtKB:  P62157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62157
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.125α = 90
b = 40.125β = 90
c = 173.814γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description