1KRM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 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.,Sect.D 59: 299-303


  • 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 mode ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
adenosine deaminase
A
356Bos taurusGene Names: ADA
EC: 3.5.4.4
Find proteins for P56658 (Bos taurus)
Go to Gene View: ADA
Go to UniProtKB:  P56658
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PRH
Query on PRH

Download SDF File 
Download CCD File 
A
6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE
C10 H15 N4 O5
WGRXVKRHIMUTPD-YOHZANMFSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.030α = 90.00
b = 80.030β = 90.00
c = 141.680γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description