MolNFT v1 · #144709 · protein + DNA

Mbd of human MECP2 in complex with methylated DNA

6C1Y · Methyl-cpg-binding protein 2: “Mbd of human MECP2 in complex with methylated DNA”. X-ray diffraction, 1 ligand (UNX), 5 pockets (best druggability 0.58). MolNFT v1 #144709 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6C1Y
Type: protein + DNA
Length: 190 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding protein 2; 12-mer DNA
UniProt: P51608
Ligands: UNX
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Methyl-cpg-binding protein 2	protein	71	20% helix, 20% strand	P51608
D, C, F, E	12-mer DNA	dna	12	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 3 copies · chains A, D, B, F, E

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

Pockets

5 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	176	0.58	0.82	24	UNX
2	153	0.55	0.81	21	UNX
3	142	0.40	0.74	14	empty
4	101	0.36	0.75	18	empty
5	62	0.35	0.78	16	empty

Interfaces

7 interfaces between chains.

F–E · 561 Å² buried · 56 hydrogen bonds · nucleic-nucleic
D–C · 554 Å² buried · 50 hydrogen bonds · nucleic-nucleic
A–C · 369 Å² buried · 8 hydrogen bonds · protein-nucleic
B–F · 354 Å² buried · 5 hydrogen bonds · protein-nucleic
A–D · 306 Å² buried · 4 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

6C1Y · mbd of human mecp2 in complex with methylated DNA · the same entry in another collection · chain D against D, 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 0.90

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 P51608
Elsewhere: RCSB PDB 6C1Y · PDBe 6C1Y · UniProt P51608

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