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Crystal structure of the de-sumoylating protease

Analyse Crystal structure of the de-sumoylating protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LNB
Type: protein
Length: 259 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-like-specific protease 2
EC: 3.4.22.68
UniProt: P40537
Pockets: 4 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Ubiquitin-like-specific protease 2 (EC 3.4.22.68)	protein	259	53% helix, 15% strand	P40537

Ligands and binding sites

ACT · Acetate ion · additive · chains B

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

Pockets

4 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	119	0.41	0.76	23	empty
2	90	0.37	0.75	18	empty
3	82	0.36	0.76	17	empty
4	54	0.33	0.77	15	empty

Compared structures

5LNB · Crystal structure of the de-sumoylating protease · the same entry in another collection · chain B against B, TM-score 1.00
P40537 · AlphaFold monomer V2.0 prediction for ubiquitin-like-specific protease 2 (P40537) · a predicted model of the same protein · chain B 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 P40537
Elsewhere: RCSB PDB 5LNB · PDBe 5LNB · UniProt P40537

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