3VYB

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence

Structural Biology Knowledgebase: 3VYB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VYB

Classification: HYDROLASE / DNA

Total Structure Weight: 16555.99


Macromolecule Entities
Molecule Chains Length Organism Details
Methyl-CpG-binding domain protein 4 A 69 Mus musculus EC#: 3.2.2 IUBMB
Fragment: methyl CpG binding domain, UNP residues 69-136
Gene Name(s): Mbd4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') B 14 synthetic
DNA (5'-D(*GP*TP*CP*(5HC)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') C 14 synthetic

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
B DNA LINKING C10 H16 N3 O7 P DC
5HC
Query on 5HC
C DNA LINKING C10 H16 N3 O8 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.191
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 88.69 α = 90.00
b = 97.76 β = 90.00
c = 55.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-22
  • 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