MolNFT v1 · #140422 · protein

Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity

5YAB: “Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity”. X-ray diffraction, 19 pockets (best druggability 0.89). MolNFT v1 #140422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YAB
Type: protein
Length: 1,469 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
UniProt: K7ZP76
Pockets: 19 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	367	38% helix, 25% strand	K7ZP76
B	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	366	38% helix, 25% strand	K7ZP76
C, D	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	368	36% helix, 24% strand	K7ZP76

Ligands and binding sites

ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1038	0.89	0.91	68	empty
2	66	0.76	1.00	16	empty
3	72	0.76	0.99	17	empty
4	492	0.71	0.81	79	ACT
5	433	0.68	0.80	55	ACT

Interfaces

6 interfaces between chains.

A–B · 1808 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 1802 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 1789 Å² buried · 50 hydrogen bonds · protein-protein
B–D · 1778 Å² buried · 52 hydrogen bonds · protein-protein
B–C · 820 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5YAB · Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity · 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 K7ZP76
Elsewhere: RCSB PDB 5YAB · PDBe 5YAB · UniProt K7ZP76

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