5SZX

Epstein-Barr virus Zta DNA binding domain homodimer in complex with methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.251 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta.

Hong, S.Wang, D.Horton, J.R.Zhang, X.Speck, S.H.Blumenthal, R.M.Cheng, X.

(2017) Nucleic Acids Res. 45: 2503-2515


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Zta transcription factor
A, B
62Epstein-Barr virus (strain B95-8)N/A
Find proteins for P03206 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03206
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM)P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3')C18synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM)P*GP*AP*TP*GP*AP*AP*G)-3')D18synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C, D
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.251 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.549α = 90.00
b = 26.732β = 97.25
c = 99.673γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
SERGUIdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection