MolNFT v1 · #170829 · protein

Otu-like deubiquitinase from legionella -LPG2529

6YK8 · Uncharacterized protein: “Otu-like deubiquitinase from legionella -LPG2529”. X-ray diffraction, 1 ligand (PT), 7 pockets (best druggability 0.59). MolNFT v1 #170829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YK8
Type: protein
Length: 542 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: Q5ZSI8
Ligands: PT
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uncharacterized protein	protein	271	66% helix, 7% strand	Q5ZSI8

Ligands and binding sites

PT · Platinum (II) ion · metal · 10 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	187	0.59	0.81	32	empty
2	257	0.58	0.79	33	empty
3	214	0.46	0.73	33	PT
4	72	0.38	0.77	12	empty
5	59	0.33	0.76	12	empty

Interfaces

1 interface between chains.

A–B · 261 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6YK8 · OTU-like deubiquitinase from Legionella -Lpg2529 · 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 Q5ZSI8
Elsewhere: RCSB PDB 6YK8 · PDBe 6YK8 · UniProt Q5ZSI8

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