MolNFT v1 · #118037 · protein

Crystal structure of chromodomain of CBX8 in complex with inhibitor UNC3866

5EQ0 · Chromobox protein homolog 8: “Crystal structure of chromodomain of CBX8 in complex with inhibitor UNC3866”. X-ray diffraction, 2 ligands (5R0, UNX). MolNFT v1 #118037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EQ0
Type: protein
Length: 60 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromobox protein homolog 8; UNC3866
UniProt: Q9HC52
Ligands: 5R0, UNX

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromobox protein homolog 8	protein	55	27% helix, 47% strand	Q9HC52
B	UNC3866	protein	5	0% helix, 60% strand	—

Ligands and binding sites

5R0 · 4-~{tert}-butylbenzoic acid · ligand · chains A, B
UNX · Unknown atom or ion · ion · 12 copies · chains A, B

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

Interfaces

1 interface between chains.

A–B · 592 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

5EQ0 · Crystal Structure of chromodomain of CBX8 in complex with inhibitor UNC3866 · the same entry in another collection · chain A against A, TM-score 1.00
Q9HC52 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 8 (Q9HC52) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q9HC52
Elsewhere: RCSB PDB 5EQ0 · PDBe 5EQ0 · UniProt Q9HC52

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