1UPQ | pdb_00001upq

Crystal structure of the pleckstrin homology (PH) domain of PEPP1

• PDB DOI: https://doi.org/10.2210/pdb1UPQ/pdb

• Classification: SIGNAL TRANSDUCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-10-09 Released: 2004-10-07 
• 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: 1.48 Å
• R-Value Free: 
  0.243 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.173 (DCC) 
• R-Value Observed: 
  0.181 (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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,011 
• Modeled Residue Count: 107 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPP1	A	123	Homo sapiens	Mutation(s): 0
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
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.243 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.173 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.547	α = 90
b = 93.547	β = 90
c = 28.786	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-07 
Deposition Author(s): Milburn, C.C., Komander, D., Deak, M., Alessi, D.R., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2004-10-07
  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: 2018-02-28
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description