5CYS | pdb_00005cys

Structure of the enzyme-product complex resulting from TDG action on a GcaC mismatch

• PDB DOI: https://doi.org/10.2210/pdb5CYS/pdb
• NAKB: 5CYS

• Classification: hydrolase/dna
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-30 Released: 2015-09-16 
• Deposition Author(s): Pozharski, E., Malik, S.S., Drohat, A.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.165 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Characterizing the enzyme-product complexes of thymine DNA glycosylase using crystallography and NMR

Malik, S.S., Varney, K.M., Pozharski, E., Drohat, A.C.

(2015) Nucleic Acids Res 

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.25 kDa 
• Atom Count: 2,948 
• Modeled Residue Count: 253 
• Deposited Residue Count: 260 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G/T mismatch-specific thymine DNA glycosylase	A	204	Homo sapiens	Mutation(s): 0  Gene Names: TDG EC: 3.2.2.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q13569 (Homo sapiens) Explore Q13569  Go to UniProtKB:  Q13569
PHAROS:  Q13569 GTEx:  ENSG00000139372

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	B [auth C]	28	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	C [auth D]	28	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.165 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.887	α = 90
b = 53.804	β = 96.07
c = 81.245	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Pozharski, E., Malik, S.S., Drohat, A.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM051074

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references