MolNFT v1 · #144706 · protein + DNA

MBD2 in complex with double-stranded DNA

6C1V · Methyl-cpg-binding domain protein 2: “MBD2 in complex with double-stranded DNA”. X-ray diffraction, 1 ligand (UNX), 6 pockets (best druggability 0.62). MolNFT v1 #144706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C1V
Type: protein + DNA
Length: 320 residues
Chains: 8
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
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F	Methyl-cpg-binding domain protein 2	protein	68	16% helix, 29% strand	Q9UBB5
B	Methyl-cpg-binding domain protein 2	protein	68	16% helix, 26% strand	Q9UBB5
C, G	12-mer DNA	dna	12	—	—
D, H	12-mer DNA	dna	12	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 36 copies · chains A, C, B, D, E, G, F, H

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	438	0.62	0.77	35	UNX
2	384	0.59	0.76	38	UNX
3	127	0.58	0.84	21	UNX
4	68	0.53	0.87	16	empty
5	132	0.43	0.75	20	UNX

Interfaces

11 interfaces between chains.

G–H · 559 Å² buried · 51 hydrogen bonds · nucleic-nucleic
C–D · 558 Å² buried · 52 hydrogen bonds · nucleic-nucleic
E–G · 375 Å² buried · 10 hydrogen bonds · protein-nucleic
A–C · 363 Å² buried · 10 hydrogen bonds · protein-nucleic
B–D · 325 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

6C1V · MBD2 in complex with double-stranded 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 6C1V · PDBe 6C1V · UniProt Q9UBB5

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