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

Analyse Crystal structure of the isomaltulose synthase smua from protaminobacter rubrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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

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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

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