MolNFT v1 · #186345 · protein + DNA

Crystal structure of MBD2 with DNA

7RAY · Methyl-cpg-binding domain protein 2: “Crystal structure of MBD2 with DNA”. X-ray diffraction, 1 ligand (UNX), 2 pockets (best druggability 0.52). MolNFT v1 #186345 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RAY
Type: protein + DNA
Length: 98 residues
Chains: 3
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*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*…
UniProt: Q9UBB5
Ligands: UNX
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl-cpg-binding domain protein 2	protein	74	15% helix, 27% strand	Q9UBB5
B, C	DNA (5'-D(GPCPCPAPA)-R(P(5MC))-D(PGPTPTPGPGPC)- 3')	dna	12	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.52	0.81	20	UNX
2	88	0.32	0.73	14	empty

Interfaces

3 interfaces between chains.

B–C · 551 Å² buried · 48 hydrogen bonds · nucleic-nucleic
A–C · 340 Å² buried · 10 hydrogen bonds · protein-nucleic
A–B · 284 Å² buried · 5 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

7RAY · Crystal structure of MBD2 with 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 0.90

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 7RAY · PDBe 7RAY · UniProt Q9UBB5

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