4LG7

Crystal structure MBD4 MBD domain in complex with methylated CpG DNA

Structural Biology Knowledgebase: 4LG7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4LG7

Classification: HYDROLASE / DNA

Total Structure Weight: 15179.97


Macromolecule Entities
Molecule Chains Length Organism Details
Methyl-CpG-binding domain protein 4 A 68 Homo sapiens EC#: 3.2.2 IUBMB
Fragment: UNP residues 83-149
Gene Name(s): MBD4 Gene View MED1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3') B, C 12 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UNX
Query on UNX

A, B, C UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
B, C DNA LINKING C10 H16 N3 O7 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.212
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 49.37 α = 90.00
b = 78.21 β = 90.00
c = 40.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-27
  • Released Date: 2013-07-17
  • Deposition author(s): Xu, C., Tempel, W., Wernimont, A.K., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History

No revisions since initial release