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Crystal structure of the CBX3 chromo shadow domain

Analyse Crystal structure of the CBX3 chromo shadow domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KUP
Type: protein
Length: 240 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromobox protein homolog 3
UniProt: Q13185
Ligands: UNX
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromobox protein homolog 3	protein	59	37% helix, 31% strand	Q13185
B	Chromobox protein homolog 3	protein	62	37% helix, 31% strand	Q13185
C	Chromobox protein homolog 3	protein	59	37% helix, 32% strand	Q13185
D	Chromobox protein homolog 3	protein	60	37% helix, 30% strand	Q13185

Ligands and binding sites

UNX · Unknown atom or ion · ion · 6 copies · chains A, B, C, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.49	0.75	28	empty

Interfaces

3 interfaces between chains.

A–B · 540 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 512 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 288 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3KUP · Crystal Structure of the CBX3 Chromo Shadow Domain · the same entry in another collection · chain D against D, TM-score 1.00
Q13185 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 3 (Q13185) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q13185
Elsewhere: RCSB PDB 3KUP · PDBe 3KUP · UniProt Q13185

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