MolNFT v1 · #140433 · protein

Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with L-glucono-1,5-lactone

5YAP: “Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with…”. X-ray diffraction, 2 ligands (NAI, 8S0), 14 pockets (best druggability 0.89). MolNFT v1 #140433 on GenesisL1: 3D structure…

PDB: 5YAP
Type: protein
Length: 1,461 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
Ligands: NAI, 8S0
Pockets: 14 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	366	39% helix, 25% strand	K7ZP76
B	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	367	40% helix, 25% strand	K7ZP76
D	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	362	39% helix, 23% strand	K7ZP76

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
8S0 · L-glucono-1,5-lactone · ligand · 3 copies · chains A, B, C, D

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

Pockets

14 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	965	0.89	0.91	66	empty
2	58	0.74	1.00	16	empty
3	57	0.74	0.99	17	empty
4	639	0.71	0.78	71	NAI, 8S0
5	570	0.70	0.79	64	NAI, 8S0

Interfaces

6 interfaces between chains.

C–D · 1871 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 1869 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 1760 Å² buried · 49 hydrogen bonds · protein-protein
B–D · 1743 Å² buried · 53 hydrogen bonds · protein-protein
A–D · 841 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5YAP · 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 5YAP · PDBe 5YAP · UniProt K7ZP76

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