1MQ0 | pdb_00001mq0

Crystal Structure of Human Cytidine Deaminase

• PDB DOI: https://doi.org/10.2210/pdb1MQ0/pdb

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


• 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: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 

Starting Model: experimental

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: https://doi.org/10.1021/jm0496279
• Primary Citation of Related Structures:  
  1MQ0


• 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 31.64 kDa 
• Atom Count: 2,020 
• Modeled Residue Count: 260 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine Deaminase	A, B	140	Homo sapiens	Mutation(s): 1  EC: 3.5.4.5
UniProt & NIH Common Fund Data Resources
Find proteins for P32320 (Homo sapiens) Explore P32320  Go to UniProtKB:  P32320
PHAROS:  P32320 GTEx:  ENSG00000158825

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.398	α = 90
b = 55.68	β = 90
c = 90.689	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection, Refinement description