MolNFT v1 · #139479 · protein

Metagenomic glucose-tolerant glycosidase

5XGZ · Beta-glycosidase: “Metagenomic glucose-tolerant glycosidase”. X-ray diffraction, 2 ligands (NI, SO4), 5 pockets (best druggability 0.74). MolNFT v1 #139479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XGZ
Type: protein
Length: 890 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glycosidase
UniProt: A0A1E1FFN6
Ligands: NI, SO4
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-glycosidase	protein	445	44% helix, 18% strand	A0A1E1FFN6

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 15 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.74	0.83	55	GOL
2	431	0.73	0.83	42	GOL
3	405	0.72	0.83	33	empty
4	54	0.37	0.80	14	empty
5	52	0.30	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 551 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5XGZ · Metagenomic glucose-tolerant glycosidase · 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 A0A1E1FFN6
Elsewhere: RCSB PDB 5XGZ · PDBe 5XGZ · UniProt A0A1E1FFN6

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