3K4S | pdb_00003k4s

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

• PDB DOI: https://doi.org/10.2210/pdb3K4S/pdb

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


• Deposited: 2009-10-06 Released: 2009-10-20 
• Deposition Author(s): Crawley, L., Cheng, R.K.Y., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

The structure of the catalytic domain of human PDE4d with 4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone

Crawley, L., Cheng, R.K.Y., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 40.46 kDa 
• Atom Count: 2,985 
• Modeled Residue Count: 329 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A	349	Homo sapiens	Mutation(s): 0  Gene Names: PDE4D, DPDE3 EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens) Explore Q08499  Go to UniProtKB:  Q08499
PHAROS:  Q08499 GTEx:  ENSG00000113448

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0MO	C [auth A]	(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one C15 H22 N2 O3 PDMUULPVBYQBBK-GFCCVEGCSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.217	α = 90
b = 83.217	β = 90
c = 148.766	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Crawley, L., Cheng, R.K.Y., Wood, M., Barker, J., Felicetti, B., Whittaker, M.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description