MBD2 in complex with a partially methylated DNA

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 30% strand (DSSP).

Ligands and binding sites

• UNX · Unknown atom or ion · ion · 24 copies · chains A, C, B, D
• SO4 · Sulfate ion · ion · chains A
• GOL · Glycerol · additive · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–C · 553 Ų buried · 51 hydrogen bonds · nucleic-nucleic
• A–C · 407 Ų buried · 9 hydrogen bonds · protein-nucleic
• B–D · 297 Ų buried · 6 hydrogen bonds · protein-nucleic
• A–B · 266 Ų buried · 4 hydrogen bonds · protein-nucleic
• C–D · 236 Ų buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

• 6C1T · MBD2 in complex with a partially methylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
• Q9UBB5 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 2 (Q9UBB5) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9UBB5
• Elsewhere: RCSB PDB 6C1T · PDBe 6C1T · UniProt Q9UBB5