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Crystal structural of CBX5 chromo shadow domain

Analyse Crystal structural of CBX5 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: 3I3C
Type: protein
Length: 229 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromobox protein homolog 5
UniProt: P45973
Ligands: NA
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chromobox protein homolog 5	protein	57	33% helix, 33% strand	P45973
B	Chromobox protein homolog 5	protein	58	33% helix, 36% strand	P45973
C	Chromobox protein homolog 5	protein	57	33% helix, 35% strand	P45973
D	Chromobox protein homolog 5	protein	57	35% helix, 39% strand	P45973

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.41	0.75	23	empty
2	57	0.33	0.77	17	empty
3	57	0.29	0.75	14	empty

Interfaces

3 interfaces between chains.

A–D · 488 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 404 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 391 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3I3C · Crystal Structural of CBX5 Chromo Shadow Domain · the same entry in another collection · chain D against D, TM-score 1.00
P45973 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 5 (P45973) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 P45973
Elsewhere: RCSB PDB 3I3C · PDBe 3I3C · UniProt P45973

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