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Crystal structure of the hepn domain from human sacsin

Analyse Crystal structure of the hepn domain from human sacsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3O10
Type: protein
Length: 551 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sacsin
UniProt: Q9NZJ4
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sacsin	protein	139	70% helix, 0% strand	Q9NZJ4
C	Sacsin	protein	136	70% helix, 0% strand	Q9NZJ4
D	Sacsin	protein	137	70% helix, 0% strand	Q9NZJ4

Ligands and binding sites

MLI · Malonate ion · additive · 3 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	397	0.60	0.76	55	empty
2	152	0.46	0.76	28	empty
3	61	0.26	0.72	17	MLI

Interfaces

4 interfaces between chains.

C–D · 1643 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1576 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 310 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 308 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3O10 · Crystal structure of the HEPN domain from human sacsin · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9NZJ4
Elsewhere: RCSB PDB 3O10 · PDBe 3O10 · UniProt Q9NZJ4

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