MolNFT v1 · #83675 · protein

Full-length beta-fructofuranosidase from microbacterium saccharophilum K-1

3WPU: “Full-length beta-fructofuranosidase from microbacterium saccharophilum K-1”. X-ray diffraction, 11 pockets (best druggability 0.73). MolNFT v1 #83675 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WPU
Type: protein
Length: 1,076 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-fructofuranosidase
EC: 3.2.1.26
UniProt: Q8VW87
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-fructofuranosidase (EC 3.2.1.26)	protein	538	15% helix, 38% strand	Q8VW87

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

11 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	1026	0.73	0.76	120	GOL
2	360	0.62	0.78	44	GOL
3	86	0.36	0.76	21	empty
4	100	0.36	0.74	20	empty
5	71	0.32	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 454 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3WPU · Full-length beta-fructofuranosidase from Microbacterium saccharophilum K-1 · 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 Q8VW87
Elsewhere: RCSB PDB 3WPU · PDBe 3WPU · UniProt Q8VW87

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