MolNFT v1 · #159167 · protein + DNA

MECP2 mbd in complex with DNA

6OGK · Methyl-cpg-binding protein 2: “MECP2 mbd in complex with DNA”. X-ray diffraction, 2 ligands (CA, UNX), 3 pockets (best druggability 0.57). MolNFT v1 #159167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OGK
Type: protein + DNA
Length: 100 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding protein 2; DNA (5'-D(*GP*CP*CP*TP*AP*(5CM)P*AP*CP*TP*CP*CP*G)-3'); DNA…
UniProt: P51608
Ligands: CA, UNX
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl-cpg-binding protein 2	protein	76	17% helix, 18% strand	P51608
D	DNA (5'-D(GPCPCPTPAP(5CM)PAPCPTPCPCPG)-3')	dna	12	—	—
C	DNA (5'-D(CPGPGPAPGPTPGPTPAPGPGPC)-3')	dna	12	—	—

Ligands and binding sites

CA · Calcium ion · metal · chains A
UNX · Unknown atom or ion · ion · 17 copies · chains A, D, C

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

Pockets

3 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	176	0.57	0.81	29	UNX
2	107	0.33	0.73	18	UNX
3	63	0.28	0.74	13	UNX

Interfaces

3 interfaces between chains.

D–C · 574 Å² buried · 62 hydrogen bonds · nucleic-nucleic
A–D · 313 Å² buried · 3 hydrogen bonds · protein-nucleic
A–C · 311 Å² buried · 13 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

6OGK · 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 0.89

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 6OGK · PDBe 6OGK · UniProt P51608

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