6E93

Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 in complex with methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.747 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.

Hudson, N.O.Whitby, F.G.Buck-Koehntop, B.A.

(2018) J. Biol. Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger and BTB domain-containing protein 38
A
119Homo sapiensMutation(s): 0 
Gene Names: ZBTB38
Find proteins for Q8NAP3 (Homo sapiens)
Go to Gene View: ZBTB38
Go to UniProtKB:  Q8NAP3
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3')C18Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3')D18Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 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: 1.747 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.804α = 90.00
b = 77.270β = 90.00
c = 103.756γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB-1715379

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release