Adenosine deaminase

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.240 

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This is version 1.3 of the entry. See complete history


Structural Basis of Compound Recognition by Adenosine Deaminase

Kinoshita, T.Nakanishi, I.Terasaka, T.Kuno, M.Seki, N.Warizaya, M.Matsumura, H.Inoue, T.Takano, K.Adachi, H.Mori, Y.Fujii, T.

(2005) Biochemistry 44: 10562-10569

  • DOI: https://doi.org/10.1021/bi050529e
  • Primary Citation of Related Structures:  
    1VFL, 1WXY

  • PubMed Abstract: 

    Structural snapshots corresponding to various states enable elucidation of the molecular recognition mechanism of enzymes. Adenosine deaminase has two distinct conformations, an open form and a closed form, although it has so far been unclear what factors influence adaptation of the alternative conformations. Herein, we have determined the first nonligated structure as an initial state, which was the open form, and have thereby rationally deduced the molecular recognition mechanism. Inspection of the active site in the nonligated and ligated states indicated that occupancy at one of the water-binding positions in the nonligated state was highly significant in determining alternate conformations. When this position is empty, subsequent movement of Phe65 toward the space induces the closed form. On the other hand, while occupied, the overall conformation remains in the open form. This structural understanding should greatly assist structure-oriented drug design and enable control of the enzymatic activity.

  • Organizational Affiliation

    Exploratory Research Laboratories, Fujisawa Pharmaceutical Company, Ltd., 5-2-3, Tokodai, Tsukuba, Ibaraki 300-2698, Japan. kinotk@b.s.osakafu-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine deaminase356Bos taurusMutation(s): 0 
Find proteins for P56658 (Bos taurus)
Explore P56658 
Go to UniProtKB:  P56658
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56658
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.240 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.726α = 90
b = 73.726β = 90
c = 134.013γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations