5VMV

Kaiso (ZBTB33) zinc finger DNA binding domain in complex with its double CpG-methylated DNA consensus binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.313 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.

Nikolova, E.N.Stanfield, R.L.Dyson, H.J.Wright, P.E.

(2018) Biochemistry 57: 2109-2120


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator Kaiso
A
134Homo sapiensGene Names: ZBTB33 (KAISO, ZNF348)
Find proteins for Q86T24 (Homo sapiens)
Go to Gene View: ZBTB33
Go to UniProtKB:  Q86T24
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')D,E18Homo sapiens
Small Molecules
Ligands 2 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
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
D, E
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.313 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.219α = 90.00
b = 183.792β = 90.00
c = 104.566γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

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: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references