Crystal structure of chromodomain of MPP8 in complex with inhibitor UNC3866

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 40% strand (DSSP).

Ligands and binding sites

• 5R0 · 4-~{tert}-butylbenzoic acid · ligand · 2 copies · chains A, C, B, D
• UNX · Unknown atom or ion · ion · 19 copies · chains A, B, D

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.

Interfaces

4 interfaces between chains.

• B–D · 554 Ų buried · 13 hydrogen bonds · protein-protein
• A–C · 506 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 234 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 97 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

• 6V2S · Crystal Structure of chromodomain of MPP8 in complex with inhibitor UNC3866 · the same entry in another collection · chain A against A, TM-score 1.00
• Q99549 · AlphaFold monomer V2.0 prediction for M-phase phosphoprotein 8 (Q99549) · a predicted model of the same protein · chain B 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 Q99549
• Elsewhere: RCSB PDB 6V2S · PDBe 6V2S · UniProt Q99549