MolNFT v1 · #64707 · protein

Crystal structure of the isomaltulose synthase smua from protaminobacter rubrum in complex with the inhibitor deoxynojirimycin

3GBE · Sucrose isomerase smua from protaminobacter rubrum: “Crystal structure of the isomaltulose synthase smua from protaminobacter rubrum in complex with the inhibitor…”. X-ray diffraction, 1 ligand (NOJ), 6 pockets (best druggability…

PDB: 3GBE
Type: protein
Length: 558 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sucrose isomerase smua from protaminobacter rubrum
EC: 5.4.99.11
Ligands: NOJ
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sucrose isomerase smua from protaminobacter rubrum (EC 5.4.99.11)	protein	558	35% helix, 18% strand	—

Ligands and binding sites

NOJ · 1-deoxynojirimycin · ligand · chains A
EDO · 1,2-ethanediol · additive · 8 copies · chains A
FLC · Citrate anion · additive · chains A

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

Pockets

6 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	116	0.78	0.97	25	EDO, NOJ
2	53	0.73	0.99	16	empty
3	171	0.55	0.80	23	empty
4	130	0.49	0.79	26	empty
5	138	0.45	0.77	23	EDO

Compared structures

3GBE · Crystal structure of the isomaltulose synthase SmuA from Protaminobacter rubrum in… · 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
Elsewhere: RCSB PDB 3GBE · PDBe 3GBE

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.