6C2F | pdb_00006c2f

MBD2 in complex with methylated DNA

• PDB DOI: https://doi.org/10.2210/pdb6C2F/pdb
• NAKB: 6C2F

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-08 Released: 2018-02-14 
• Deposition Author(s): Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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 (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.79 kDa 
• Atom Count: 5,915 
• Modeled Residue Count: 552 
• Deposited Residue Count: 618 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 2	A, D, G, J, M, P	79	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
12-mer DNA	B, E, H, K, N, Q	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
12-mer DNA	C, F, I, L, O, R	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	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 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36C2F

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.51	α = 90.07
b = 40.6	β = 93.11
c = 202.38	γ = 119.75

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-10-22
  Changes: Database references, Derived calculations, Structure summary