MolNFT v1 · #182563 · protein + DNA

Crystal structure of MBD2 with DNA

7MWM · Methyl-cpg-binding domain protein 2: “Crystal structure of MBD2 with DNA”. X-ray diffraction, 1 ligand (UNX), 6 pockets (best druggability 0.70). MolNFT v1 #182563 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MWM
Type: protein + DNA
Length: 196 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*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*…
UniProt: Q9UBB5
Ligands: UNX
Pockets: 6 · best druggability 0.70

Structure

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

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

Ligands and binding sites

UNX · Unknown atom or ion · ion · 35 copies · chains A, C, B, E, D, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	370	0.70	0.83	31	UNX
2	170	0.60	0.83	22	UNX
3	180	0.58	0.82	26	empty
4	113	0.38	0.74	25	UNX
5	54	0.26	0.74	9	UNX

Interfaces

9 interfaces between chains.

E–F · 550 Å² buried · 50 hydrogen bonds · nucleic-nucleic
C–D · 546 Å² buried · 49 hydrogen bonds · nucleic-nucleic
B–E · 357 Å² buried · 7 hydrogen bonds · protein-nucleic
A–C · 307 Å² buried · 4 hydrogen bonds · protein-nucleic
A–D · 271 Å² buried · 7 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

7MWM · 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 0.91

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 7MWM · PDBe 7MWM · UniProt Q9UBB5

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