1UPR | pdb_00001upr

Crystal structure of the PEPP1 pleckstrin homology domain in complex with Inositol 1,3,4,5-tetrakisphosphate

• PDB DOI: https://doi.org/10.2210/pdb1UPR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2003-10-10 Released: 2004-10-20 
• Deposition Author(s): Milburn, C.C., Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.276 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Pleckstrin Homology Domain of Pepp1

Milburn, C.C., Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.64 kDa 
• Atom Count: 937 
• Modeled Residue Count: 107 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY A MEMBER 4	A	123	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4M7 (Homo sapiens) Explore Q9H4M7  Go to UniProtKB:  Q9H4M7
PHAROS:  Q9H4M7 GTEx:  ENSG00000105559

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4IP	B [auth A]	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C6 H16 O18 P4 CIPFCGZLFXVXBG-CNWJWELYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.276 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.577	α = 90
b = 92.577	β = 90
c = 35.571	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-20 
Deposition Author(s): Milburn, C.C., Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

Revision History  

• Version 1.0: 2004-10-20
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2016-12-07
  Changes: Database references
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description