3VYQ

Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1

Structural Biology Knowledgebase: 3VYQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 3VYQ

Classification: HYDROLASE / DNA

Total Structure Weight: 23660.07


Macromolecule Entities
Molecule Chains Length Organism Details
Methyl-CpG-binding domain protein 4 A, D 74 Mus musculus EC#: 3.2.2 IUBMB
Fragment: methyl CpG binding domain, UNP residues 63-136
Gene Name(s): Mbd4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3') B 11 synthetic
DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3') C 11 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
B DNA LINKING C10 H16 N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.193
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 30.60 α = 75.28
b = 34.09 β = 77.76
c = 61.17 γ = 87.31

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-02
  • Released Date: 2013-01-16
  • Deposition author(s): Otani, J., Arita, K., Kato, T., Kinoshita, M., Ariyoshi, M., Shirakawa, M.

Revision History

  • 2013-08-14
    Type: Citation | Details: Citation update