6C2F

MBD2 in complex with methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

MBD2 in complex with methylated DNA

Liu, K.Xu, C.Tempel, W.Arrowsmith, C.H.Bountra, C.Edwards, A.M.Min, J.Structural Genomics Consortium

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-CpG-binding domain protein 2
A, D, G, J, M
A, D, G, J, M, P
79Homo sapiensMutation(s): 0 
Gene Names: MBD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBB5 (Homo sapiens)
Explore Q9UBB5 
Go to UniProtKB:  Q9UBB5
PHAROS:  Q9UBB5
GTEx:  ENSG00000134046 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBB5
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
12-mer DNA
B, E, H, K, N
B, E, H, K, N, Q
12synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
12-mer DNA
C, F, I, L, O
C, F, I, L, O, R
12synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth M]
BA [auth M]
CA [auth P]
S [auth A]
T [auth A]
AA [auth M],
BA [auth M],
CA [auth P],
S [auth A],
T [auth A],
U [auth D],
V [auth D],
W [auth G],
X [auth G],
Y [auth J],
Z [auth J]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M36C2F
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.51α = 90.07
b = 40.6β = 93.11
c = 202.38γ = 119.75
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description