MolNFT v1 · #25689 · protein

Beta-fructosidase from thermotoga maritima in complex with raffinose

1W2T · Beta fructosidase: “Beta-fructosidase from thermotoga maritima in complex with raffinose”. X-ray diffraction, 4 ligands (GLC, FRU, GLA), 20 pockets (best druggability 0.76). MolNFT v1 #25689 on GenesisL1: 3D structure, binding sites…

PDB: 1W2T
Type: protein
Length: 2,592 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta fructosidase
EC: 3.2.1.26
UniProt: O33833
Ligands: GLC, FRU, GLA, SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Beta fructosidase (EC 3.2.1.26)	protein	432	3% helix, 58% strand	O33833

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
FRU · beta-D-fructofuranose · sugar · 6 copies · chains A, B, C, D, E, F
GLA · alpha-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 4 copies · chains B, C, E
CIT · Citric acid · additive · chains A

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.76	0.79	82	SO4
2	552	0.71	0.80	75	empty
3	612	0.69	0.78	48	empty
4	364	0.69	0.82	50	empty
5	584	0.66	0.76	60	empty

Interfaces

8 interfaces between chains.

D–E · 1233 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 645 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 623 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 533 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 459 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1W2T · beta-fructosidase from Thermotoga maritima in complex with raffinose · the same entry in another collection · chain F against F, TM-score 1.00
O33833 · AlphaFold monomer V2.0 prediction for beta-fructosidase (O33833) · a predicted model of the same protein · chain F 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 O33833
Elsewhere: RCSB PDB 1W2T · PDBe 1W2T · UniProt O33833

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