Research workbench

MBD2 in complex with methylated DNA

Analyse MBD2 in complex with methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CNQ
Type: protein + DNA
Length: 184 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding domain protein 2; DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*TP*TP*GP*GP*C)-3'…
UniProt: Q9UBB5
Ligands: UNX
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Methyl-cpg-binding domain protein 2	protein	68	16% helix, 29% strand	Q9UBB5
D, C, E, F	DNA (5'-D(GPCPCPAPAP(5CM)PGPTPTPGPGPC)-3')	dna	12	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 4 copies · chains A, B, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.54	0.83	21	empty
2	107	0.52	0.82	20	empty
3	116	0.37	0.74	16	UNX

Interfaces

7 interfaces between chains.

D–C · 552 Å² buried · 54 hydrogen bonds · nucleic-nucleic
E–F · 548 Å² buried · 56 hydrogen bonds · nucleic-nucleic
B–F · 371 Å² buried · 11 hydrogen bonds · protein-nucleic
A–C · 369 Å² buried · 11 hydrogen bonds · protein-nucleic
A–B · 358 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

6CNQ · MBD2 in complex with methylated DNA · the same entry in another collection · chain D against D, 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 6CNQ · PDBe 6CNQ · UniProt Q9UBB5

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