6CC8

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure MBD3 MBD domain in complex with methylated CpG DNA

Liu, K.Tempel, W.Bountra, C.Arrowsmith, C.H.Edwards, A.M.Min, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl-CpG-binding domain protein 3
A, B
73Homo sapiensGene Names: MBD3
Find proteins for O95983 (Homo sapiens)
Go to Gene View: MBD3
Go to UniProtKB:  O95983
Entity ID: 2
MoleculeChainsLengthOrganism
methylated CpG DNAC,D,E,F12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C, E
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
UNK
Query on UNK

Download SDF File 
Download CCD File 
F
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C, D, E, F
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.550α = 90.00
b = 36.640β = 92.77
c = 130.930γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release