3KM8

Crystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine

• PDB DOI: https://doi.org/10.2210/pdb3KM8/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-10 Released: 2010-10-20 
• Deposition Author(s): Fan, X., Gao, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

The Catalytic Mechanism of Adenosine Deaminase from Mouse: An Experimental and Theoretical Study

Wu, X., Fan, X., Gao, Y., Su, X., Zhang, H., Wu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.69 kDa 
• Atom Count: 5,972 
• Modelled Residue Count: 698 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A, B	352	Mus musculus	Mutation(s): 2  Gene Names: Ada EC: 3.5.4.4
UniProt
Find proteins for P03958 (Mus musculus) Explore P03958  Go to UniProtKB:  P03958

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9DI	C [auth A], E [auth B]	9-DEAZAINOSINE C11 H13 N3 O5 WKDMPDYUJKSXBW-KBHCAIDQSA-N
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.337	α = 90
b = 93.616	β = 97.35
c = 85.416	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Fan, X., Gao, Y.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description