Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.05 kDa 
• Atom Count: 2,922 
• Modelled Residue Count: 349 
• Deposited Residue Count: 349 
• Unique protein chains: 1

 1ADD

A PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADENOSINE DEAMINASE WITH BOUND 1-DEAZA-ADENOSINE AND ZINC-ACTIVATED WATER

• PDB DOI:  https://doi.org/10.2210/pdb1ADD/pdb

• Classification: HYDROLASE(ACTING IN CYCLICAMIDINES)
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1992-12-22 Released: 1994-01-31 
• Deposition Author(s): Wilson, D.K., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Literature

A pre-transition-state mimic of an enzyme: X-ray structure of adenosine deaminase with bound 1-deazaadenosine and zinc-activated water.

Wilson, D.K., Quiocho, F.A.

(1993) Biochemistry 32: 1689-1694

• PubMed: 8439534 
• DOI: https://doi.org/10.1021/bi00058a001
• Primary Citation of Related Structures:  
  1ADD


• PubMed Abstract: 
  

The refined 2.4-A structure of adenosine deaminase, recently discovered to be a zinc metalloenzyme [Wilson, D. K., Rudolph, F. B., & Quiocho, F. A. (1991) Science 252, 1278-1284], complexed with the ground-state analog 1-deazaadenosine shows the mode of binding of the analog and, unexpectedly, a zinc-activated water (hydroxide). This structure of a pre-transition-state mimic, combined with that previously determined for the complex with 6(R)-hydroxy-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, sheds new understanding of the precise stereospecificity and hydrolytic catalysis of an important and well-characterized member of a large group of zinc metalloenzymes. As both of these excellent mimics were generated in the active site, they demonstrate a powerful means of dissecting the course of an enzymatic reaction by direct crystallographic analysis.

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Related Citations: 

• Atomic Structure of Adenosine Deaminase Complexed with a Transition Analog: Understanding Catalysis and Immunodeficiency Mutations
  Wilson, D.K., Rudolph, F.B., Quiocho, F.A.
  (1991) Science 252: 1278

• Preliminary X-Ray Analysis of Murine Adenosine Deaminase
  Wilson, D.K., Rudolph, F.B., Harrison, M.L., Kellems, R.E., Quiocho, F.A.
  (1988) J Mol Biol 200: 613

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Organizational Affiliation: 

Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENOSINE DEAMINASE	A	349	Mus musculus	Mutation(s): 0  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
1DA	C [auth A]	1-DEAZA-ADENOSINE C11 H14 N4 O4 NVUDDRWKCUAERS-PNHWDRBUSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1DA	PDBBind:  1ADD	Ki: 180 (nM) from 1 assay(s)
	Binding MOAD:  1ADD	Ki: 180 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.39	α = 90
b = 94.28	β = 127.05
c = 73.02	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Wilson, D.K., Quiocho, F.A.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance