5NNU

KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping.

Earl, C.Bagneris, C.Zeman, K.Cole, A.Barrett, T.Savva, R.

(2018) Nucleic Acids Res. 46: 4286-4300


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A, B, D, E
240Human herpesvirus 8 type P (isolate GK18)Mutation(s): 0 
Gene Names: ORF46
EC: 3.2.2.27
Find proteins for F5HFA1 (Human herpesvirus 8 type P (isolate GK18))
Go to UniProtKB:  F5HFA1
Entity ID: 1
MoleculeChainsLengthOrganism
DNA containing an abasic siteS,U,W,Y11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNAT,V,X,Z11synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AAB
Query on AAB
S, U, W, Y
DNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.100α = 90.00
b = 70.800β = 94.36
c = 140.250γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references