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Crystal structure of chromobox homolog 7 (CBX7) chromodomain with H3K27ME3 peptide

Analyse Crystal structure of chromobox homolog 7 (CBX7) chromodomain with H3K27ME3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X3K
Type: protein
Length: 142 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromobox protein homolog 7; H3K27ME3 peptide
UniProt: Q8VDS3
Ligands: NI, K
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Chromobox protein homolog 7	protein	64	33% helix, 39% strand	Q8VDS3
C, D	H3K27ME3 peptide	protein	7	0% helix, 43% strand	—

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
K · Potassium ion · metal · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	228	0.55	0.78	29	empty

Interfaces

3 interfaces between chains.

B–D · 680 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 675 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 316 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (methylation).

Compared structures

4X3K · Crystal structure of chromobox homolog 7 (CBX7) chromodomain with H3K27me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q8VDS3 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 7 (Q8VDS3) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 Q8VDS3
Elsewhere: RCSB PDB 4X3K · PDBe 4X3K · UniProt Q8VDS3

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