MolNFT v1 · #182561 · protein + DNA

Crystal structure of MBD2 with DNA

7MWK · Methyl-cpg-binding domain protein 2: “Crystal structure of MBD2 with DNA”. X-ray diffraction, 1 ligand (UNX), 3 pockets (best druggability 0.57). MolNFT v1 #182561 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MWK
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*(MC)P*GP*TP*TP*GP*GP*C)-3')
UniProt: Q9UBB5
Ligands: UNX
Pockets: 3 · best druggability 0.57

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
C, D, E, F	DNA (5'-D(GPCPCPAPAP(MC)PGPTPTPGPGPC)-3')	dna	12	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 4 copies · chains 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	0.57	0.85	22	empty
2	107	0.52	0.83	18	empty
3	114	0.40	0.76	16	UNX

Interfaces

7 interfaces between chains.

E–F · 550 Å² buried · 60 hydrogen bonds · nucleic-nucleic
C–D · 543 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–B · 357 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 334 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 327 Å² buried · 11 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

7MWK · Crystal structure of MBD2 with DNA · the same entry in another collection · chain C against C, 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 7MWK · PDBe 7MWK · UniProt Q9UBB5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.