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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: 6C1A
Type: protein + DNA
Length: 319 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding domain protein 2; DNA strand 1; Complement to DNA strand 1
UniProt: Q9UBB5
Ligands: UNX
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 5 distinct chains · 16% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl-cpg-binding domain protein 2	protein	68	16% helix, 29% strand	Q9UBB5
B	Methyl-cpg-binding domain protein 2	protein	67	16% helix, 30% strand	Q9UBB5
C, G	DNA strand 1	dna	12	—	—
D, H	Complement to DNA strand 1	dna	12	—	—
E, F	Methyl-cpg-binding domain protein 2	protein	68	16% helix, 29% strand	Q9UBB5

Ligands and binding sites

UNX · Unknown atom or ion · ion · 52 copies · chains A, C, D, B, E, G, H, F

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	366	0.61	0.77	35	UNX
2	368	0.60	0.77	39	UNX
3	62	0.58	0.90	19	UNX
4	105	0.56	0.85	21	UNX
5	144	0.45	0.76	20	UNX

Interfaces

11 interfaces between chains.

C–D · 558 Å² buried · 48 hydrogen bonds · nucleic-nucleic
G–H · 553 Å² buried · 50 hydrogen bonds · nucleic-nucleic
A–C · 366 Å² buried · 6 hydrogen bonds · protein-nucleic
E–G · 358 Å² buried · 7 hydrogen bonds · protein-nucleic
B–D · 320 Å² buried · 7 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

6C1A · MBD2 in complex with methylated DNA · the same entry in another collection · chain H against H, 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 6C1A · PDBe 6C1A · UniProt Q9UBB5

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