Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 31636.71 
• Atom Count: 1958 
• Residue Count: 280 
• Unique protein chains: 1

1MQ0

Crystal Structure of Human Cytidine Deaminase

• DOI: 10.2210/pdb1MQ0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• Deposited: 2002-09-13 Released: 2003-11-04 
• Deposition Author(s): Chung, S.J., Fromme, J.C., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.262 
• R-Value Work: 0.217 

Literature

Structure of human cytidine deaminase bound to a potent inhibitor

Chung, S.J., Fromme, J.C., Verdine, G.L.

(2005) J.Med.Chem. 48: 658-660

• PubMed: 15689149 
• DOI: 10.1021/jm0496279


• PubMed Abstract: 
  

Human cytidine deaminase (CDA) is an enzyme prominent for its role in catalyzing metabolic processing of nucleoside-type anticancer and antiviral agents. It is thus a promising target for the development of small molecule therapeutic adjuvants. We report the first crystal structure of human CDA as a complex with a tight-binding inhibitor, diazepinone riboside 1. The structure reveals that inhibitor 1 is able to establish a canonical pi/pi-interaction with a key active site residue, Phe 137.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytidine Deaminase	A, B	140	Homo sapiens	Mutation(s): 1  Gene Names: CDA (CDD) EC: 3.5.4.5
Find proteins for P32320 (Homo sapiens) Go to Gene View: CDA Go to UniProtKB:  P32320

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BRD	A, B	1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE C10 H14 N2 O5 MEPCJRCEYSZBDO-FNCVBFRFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.262 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 52.398	α = 90.00
b = 55.680	β = 90.00
c = 90.689	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data scaling
CrystalClear	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-13 
• Released Date: 2003-11-04 
• Deposition Author(s): Chung, S.J., Fromme, J.C., Verdine, G.L.

Revision History 

• Version 1.0: 2003-11-04
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description