6CEU

MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.005 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data

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 sapiensMutation(s): 0 
Gene Names: MBD3
Find proteins for O95983 (Homo sapiens)
Go to Gene View: MBD3
Go to UniProtKB:  O95983
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3')C,E12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3')D,F12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
C, D, E
UNKNOWN ATOM OR ION
X
*
 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

Unit Cell:
Length (Å)Angle (°)
a = 72.174α = 90.00
b = 36.223β = 92.85
c = 131.157γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
REFMACphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release