2I5F

Crystal structure of the C-terminal PH domain of pleckstrin in complex with D-myo-Ins(1,2,3,5,6)P5

• PDB DOI: https://doi.org/10.2210/pdb2I5F/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-24 Released: 2007-08-07 
• Deposition Author(s): Jackson, S.G., Haslam, R.J., Junop, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

Structural analysis of the carboxy terminal PH domain of pleckstrin bound to D-myo-inositol 1,2,3,5,6-pentakisphosphate.

Jackson, S.G., Zhang, Y., Haslam, R.J., Junop, M.S.

(2007) BMC Struct Biol 7: 80-80

• PubMed: 18034889 
• DOI: https://doi.org/10.1186/1472-6807-7-80
• Primary Citation of Related Structures:  
  2I5C, 2I5F


• PubMed Abstract: 
  

  Pleckstrin homology (PH) domains are one of the most prevalent domains in the human proteome and represent the major phosphoinositide-binding module. These domains are often found in signaling proteins and function predominately by targeting their host proteins to the cell membrane. Inositol phosphates, which are structurally similar to phosphoinositides, are not only known to play a role as signaling molecules but are also capable of being bound by PH domains.

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Organizational Affiliation: 

Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.03 kDa 
• Atom Count: 999 
• Modelled Residue Count: 99 
• Deposited Residue Count: 109 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pleckstrin	A	109	Homo sapiens	Mutation(s): 0  Gene Names: PLEK, P47
UniProt & NIH Common Fund Data Resources
Find proteins for P08567 (Homo sapiens) Explore P08567  Go to UniProtKB:  P08567
PHAROS:  P08567 GTEx:  ENSG00000115956

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5IP	B [auth A]	(1R,2R,3R,4R,5S,6S)-6-HYDROXYCYCLOHEXANE-1,2,3,4,5-PENTAYL PENTAKIS[DIHYDROGEN (PHOSPHATE)] C6 H17 O21 P5 CTPQAXVNYGZUAJ-RTWKJESVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5IP	PDBBind:  2I5F	IC50: 7500 (nM) from 1 assay(s)
	Binding MOAD:  2I5F	IC50: 2200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.15	α = 90
b = 47.7	β = 90
c = 64.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CBASS	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Jackson, S.G., Haslam, R.J., Junop, M.S.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations