2DYN

DYNAMIN (PLECKSTRIN HOMOLOGY DOMAIN) (DYNPH)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the pleckstrin homology domain from dynamin.

Timm, D., Salim, K., Gout, I., Guruprasad, L., Waterfield, M., Blundell, T.

(1994) Nat Struct Biol 1: 782-788

  • DOI: https://doi.org/10.1038/nsb1194-782
  • Primary Citation of Related Structures:  
    2DYN

  • PubMed Abstract: 

    The pleckstrin homology (PH) domain is a conserved module present in many signal transducing and cytoskeletal proteins. Here we report the 2.8 A crystal structure of the PH domain from dynamin. This domain consists of seven beta-strands forming two roughly orthogonal antiparallel beta-sheets terminating with an amphipathic alpha-helix. The structure also reveals a non-covalent dimeric association of the PH domain and a hydrophobic pocket surrounded by a charged rim. The dynamin PH domain structure is discussed in relation to its potential role in mediating interactions between proteins.

    • Organizational Affiliation: 

    Department of Crystallography, Birkbeck College, London, UK.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DYNAMIN
A, B
122Homo sapiensMutation(s): 0 
EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q05193 (Homo sapiens)
Explore Q05193 
Go to UniProtKB:  Q05193
PHAROS:  Q05193
GTEx:  ENSG00000106976 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05193
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.02α = 90
b = 86.02β = 90
c = 137.62γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 1997-11-12 
    • Deposition Author(s): Timm, D.E.

Revision History  (Full details and data files)

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Other