SMTL ID : 4l8v.1

Crystal Structure of A12K/D35S mutant myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 16 residues within 4Å: Chain A: G.11, K.12, I.13, T.73, S.74, W.75, G.76, H.79, E.96, K.97, P.98, G.124, M.126, H.176, W.272, Y.280 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.272 Hydrogen bonds: A:K.12, A:I.13, A:S.74, A:E.96, A:Y.280 Water bridges: A:G.14, A:M.126 Salt bridges: A:K.12 pi-Stacking: A:W.75, A:W.75, A:W.75 pi-Cation interactions: A:K.97 NAP.4: 16 residues within 4Å: Chain B: G.11, K.12, I.13, T.73, S.74, W.75, G.76, H.79, E.96, K.97, P.98, G.124, M.126, H.176, W.272, Y.280 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.13, B:W.272, B:W.272 Hydrogen bonds: B:K.12, B:I.13, B:S.74, B:W.75, B:E.96, B:K.97, B:Y.280 Water bridges: B:G.14 pi-Stacking: B:W.75 NAP.5: 16 residues within 4Å: Chain C: G.11, K.12, I.13, T.73, S.74, W.75, G.76, H.79, E.96, K.97, P.98, G.124, M.126, H.176, W.272, Y.280 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.13, C:W.272 Hydrogen bonds: C:K.12, C:I.13, C:W.75, C:H.79, C:E.96 Water bridges: C:M.126 Salt bridges: C:K.12, C:K.12 NAP.8: 20 residues within 4Å: Chain D: G.9, T.10, G.11, K.12, I.13, S.35, N.37, T.73, S.74, W.75, G.76, H.79, E.96, K.97, P.98, G.124, M.126, H.176, W.272, Y.280 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.272, D:W.272 Hydrogen bonds: D:T.10, D:K.12, D:I.13, D:N.37, D:W.75, D:H.79, D:E.96 pi-Stacking: D:W.75

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: D.130, S.131, G.132, L.250, P.251, R.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.132, A:R.275, A:R.275 Water bridges: A:D.130, A:D.130 EDO.3: 6 residues within 4Å: Chain A: Y.129, D.130, S.131, A.278, A.279, V.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.130, A:S.131 Water bridges: A:A.279 EDO.6: 8 residues within 4Å: Chain C: S.191, V.192, Q.193, V.214, E.216, K.324 Chain D: Q.193, I.195 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.193, C:S.191, C:E.216 EDO.7: 7 residues within 4Å: Chain A: S.254 Chain C: D.130, S.131, G.132, L.250, P.251, R.275 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.132, C:R.275, C:R.275 Water bridges: C:D.130 EDO.9: 6 residues within 4Å: Chain D: D.130, S.131, G.132, L.250, P.251, R.275 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.131, D:G.132, D:R.275, D:R.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, H. et al., Converting NAD-Specific Inositol Dehydrogenase to an Efficient NADP-Selective Catalyst, with a Surprising Twist. Biochemistry (2013)

Release Date

2013-09-04

Peptides

Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase