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MECP2 mbd in complex with DNA

Analyse MECP2 mbd in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OGJ
Type: protein + DNA
Length: 183 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding protein 2; DNA (5'-D(*CP*GP*GP*AP*GP*TP*GP*TP*AP*GP*GP*C)-3'); DNA…
UniProt: P51608
Ligands: UNX
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl-cpg-binding protein 2	protein	77	17% helix, 18% strand	P51608
B	Methyl-cpg-binding protein 2	protein	82	20% helix, 17% strand	P51608
D	DNA (5'-D(CPGPGPAPGPTPGPTPAPGPGPC)-3')	dna	12	—	—
C	DNA (5'-D(GPCPCPTPAPCPAPCPTPCPCPG)-3')	dna	12	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 8 copies · chains A, C, B, 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	687	0.70	0.78	53	UNX
2	164	0.56	0.81	31	UNX

Interfaces

5 interfaces between chains.

D–C · 553 Å² buried · 52 hydrogen bonds · nucleic-nucleic
A–D · 376 Å² buried · 13 hydrogen bonds · protein-nucleic
B–C · 348 Å² buried · 5 hydrogen bonds · protein-nucleic
A–C · 297 Å² buried · 2 hydrogen bonds · protein-nucleic
B–D · 176 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

6OGJ · MeCP2 MBD in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
P51608 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding protein 2 (P51608) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P51608
Elsewhere: RCSB PDB 6OGJ · PDBe 6OGJ · UniProt P51608

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