MolNFT v1 · #144704 · protein + DNA

MBD2 in complex with a partially methylated DNA

6C1T · Methyl-cpg-binding domain protein 2: “MBD2 in complex with a partially methylated DNA”. X-ray diffraction, 2 ligands (UNX, SO4), 2 pockets (best druggability 0.61). MolNFT v1 #144704 on GenesisL1: 3D structure, binding sites and…

PDB: 6C1T
Type: protein + DNA
Length: 157 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding domain protein 2; 12-mer DNA
UniProt: Q9UBB5
Ligands: UNX, SO4
Pockets: 2 · best druggability 0.61

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl-cpg-binding domain protein 2	protein	67	16% helix, 30% strand	Q9UBB5
B	12-mer DNA	dna	12	—	—
C	12-mer DNA	dna	12	—	—
D	Methyl-cpg-binding domain protein 2	protein	66	17% helix, 30% strand	Q9UBB5

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	401	0.61	0.77	37	UNX
2	122	0.54	0.82	23	UNX

Interfaces

5 interfaces between chains.

B–C · 553 Å² buried · 51 hydrogen bonds · nucleic-nucleic
A–C · 407 Å² buried · 9 hydrogen bonds · protein-nucleic
B–D · 297 Å² buried · 6 hydrogen bonds · protein-nucleic
A–B · 266 Å² buried · 4 hydrogen bonds · protein-nucleic
C–D · 236 Å² 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

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