2C56

A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1

• PDB DOI: https://doi.org/10.2210/pdb2C56/pdb

• Classification: HYDROLASE
• Organism(s): Human alphaherpesvirus 1
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-10-26 Released: 2005-11-28 
• Deposition Author(s): Krusong, K., Carpenter, E.P., Bellamy, S.R.W., Savva, R., Baldwin, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.212 
• R-Value Work: 0.151 
• R-Value Observed: 0.151 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 27.68 kDa 
• Atom Count: 2,102 
• Modelled Residue Count: 228 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URACIL DNA GLYCOSYLASE	A	244	Human alphaherpesvirus 1	Mutation(s): 2  EC: 3.2.2.3
UniProt
Find proteins for P10186 (Human herpesvirus 1 (strain 17)) Explore P10186  Go to UniProtKB:  P10186

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.212 
• R-Value Work: 0.151 
• R-Value Observed: 0.151 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.04	α = 90
b = 61.117	β = 92.25
c = 43.392	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-28 
Deposition Author(s): Krusong, K., Carpenter, E.P., Bellamy, S.R.W., Savva, R., Baldwin, G.S.

Revision History  

• Version 1.0: 2005-11-28
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Derived calculations, Other, Structure summary, Version format compliance
• Version 1.2: 2019-05-22
  Changes: Data collection, Other, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary