1KRM

Crystal structure of bovine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine riboside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6-dihydropurine riboside.

Kinoshita, T.Nishio, N.Nakanishi, I.Sato, A.Fujii, T.

(2003) Acta Crystallogr D Biol Crystallogr 59: 299-303

  • DOI: 10.1107/s090744490202190x
  • Primary Citation of Related Structures:  
    1KRM

  • PubMed Abstract: 
  • The crystal structure of adenosine deaminase (ADA) from bovine intestine complexed with a transition-state analogue, 6-hydroxy-1,6-dihydropurine riboside (HDPR), was solved at 2.5 A resolution by the molecular-replacement method using a homology model ba ...

    The crystal structure of adenosine deaminase (ADA) from bovine intestine complexed with a transition-state analogue, 6-hydroxy-1,6-dihydropurine riboside (HDPR), was solved at 2.5 A resolution by the molecular-replacement method using a homology model based on the crystal structure of mouse ADA. The final refinement converged to a crystallographic R factor of 20.7%. The C(alpha) backbone of bovine ADA is mostly superimposable on that of mouse ADA, although mouse ADA itself did not lead to a solution by molecular replacement. HDPR tightly interacts with ADA by means of six hydrogen bonds and is entirely enclosed within the active site. The lid of the envelope consists of two components: one contains two leucine residues, Leu55 and Leu59, and the other contains the backbone atoms Asp182 and Glu183. The C(delta) atoms of the two leucine residues are 3.5 A from the respective N atoms of the backbone. A weak interaction, similar to CH-pi binding, might make it possible to open the lid. Taking account of the movement and observation of this structural feature, the aim is to design novel ADA inhibitors.


    Organizational Affiliation

    Exploratory Research Laboratories, Fujisawa Pharmaceutical Co. Ltd, 5-2-3 Tokodai, Tsukuba, Ibaraki 300-2698, Japan. takayoshi_kinoshita@po.fujisawa.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
adenosine deaminase A356Bos taurusMutation(s): 0 
Gene Names: ADA
EC: 3.5.4.4
Find proteins for P56658 (Bos taurus)
Explore P56658 
Go to UniProtKB:  P56658
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRH
Query on PRH

Download Ideal Coordinates CCD File 
A
6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE
C10 H15 N4 O5
WGRXVKRHIMUTPD-YOHZANMFSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.03α = 90
b = 80.03β = 90
c = 141.68γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2002-01-10 
  • Released Date: 2003-01-14 
  • Deposition Author(s): Kinoshita, T.

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description