MolNFT v1 · #154996 · protein

Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NAD and myo-inositol, from paracoccus laeviglucosivorans

6KTL · Scyllo-inositol dehydrogenase with L-glucose dehydrogenase…: “Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NAD and myo-inositol, from…”. X-ray diffraction, 2 ligands (NAD, INS), 17 pockets (best…

PDB: 6KTL
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
Ligands: NAD, INS
Pockets: 17 · 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	39% helix, 25% strand	K7ZP76
C, D	Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity	protein	368	38% helix, 25% strand	K7ZP76

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · chains C, D
ACT · Acetate ion · additive · 3 copies · chains A, B, C

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

Pockets

17 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	1024	0.89	0.91	69	empty
2	70	0.76	0.99	20	empty
3	61	0.75	0.99	16	empty
4	518	0.66	0.77	58	NAD, INS
5	549	0.65	0.77	69	NAD, ACT

Interfaces

6 interfaces between chains.

C–D · 1876 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 1830 Å² buried · 40 hydrogen bonds · protein-protein
B–D · 1806 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 1762 Å² buried · 51 hydrogen bonds · protein-protein
A–D · 826 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6KTL · Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NAD and… · 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 6KTL · PDBe 6KTL · UniProt K7ZP76

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