2DYN

DYNAMIN (PLECKSTRIN HOMOLOGY DOMAIN) (DYNPH)

• PDB DOI:  https://doi.org/10.2210/pdb2DYN/pdb

• Classification: SIGNAL TRANSDUCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-07-21 Released: 1997-11-12 
• Deposition Author(s): Timm, D.E.

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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 

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

• PubMed: 7634088 
• 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.

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Organizational Affiliation: 

Department of Crystallography, Birkbeck College, London, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.86 kDa 
• Atom Count: 1,923 
• Modelled Residue Count: 222 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYNAMIN	A, B	122	Homo sapiens	Mutation(s): 0  Gene Names: DNM1, DNM 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

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 = 86.02	α = 90
b = 86.02	β = 90
c = 137.62	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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