SMTL ID : 3ntr.1 (1 other biounit)

Crystal structure of K97V mutant of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NAD and inositol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: I.8, G.9, G.11, A.12, I.13, G.14, T.34, D.35, V.36, N.37, T.73, S.74, W.75, G.76, A.78, H.79, S.82, E.96, V.97, P.98, G.124, M.126, H.176, W.272, Y.280 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.13, A:W.272 Hydrogen bonds: A:A.12, A:I.13, A:G.14, A:V.36, A:N.37, A:S.74, A:W.75, A:S.82, A:S.82, A:V.97, A:G.124 NAD.3: 22 residues within 4Å: Chain B: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, N.37, S.74, W.75, G.76, A.78, H.79, E.96, V.97, P.98, G.124, M.126, H.176, W.272, Y.280 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.272 Hydrogen bonds: B:A.12, B:I.13, B:V.36, B:N.37, B:S.74, B:W.75, B:W.75, B:A.78, B:E.96, B:Y.280 Water bridges: B:G.11, B:G.11, B:T.34 NAD.5: 25 residues within 4Å: Chain C: I.8, G.9, G.11, A.12, I.13, G.14, T.34, D.35, V.36, N.37, T.73, S.74, W.75, G.76, A.78, H.79, S.82, E.96, V.97, P.98, G.124, M.126, H.176, W.272, Y.280 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.13, C:W.272 Hydrogen bonds: C:A.12, C:I.13, C:G.14, C:V.36, C:N.37, C:S.74, C:W.75, C:S.82, C:S.82, C:V.97, C:G.124, C:Y.280 NAD.7: 22 residues within 4Å: Chain D: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, N.37, S.74, W.75, G.76, A.78, H.79, E.96, V.97, P.98, G.124, M.126, H.176, W.272, Y.280 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.272 Hydrogen bonds: D:A.12, D:I.13, D:V.36, D:N.37, D:S.74, D:W.75, D:W.75, D:A.78, D:E.96 Water bridges: D:G.11, D:G.11

4 x INS: 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE(Non-covalent)

INS.2: 5 residues within 4Å: Chain A: H.155, N.157, D.172, T.173, H.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.157, A:D.172 Water bridges: A:Y.235 INS.4: 5 residues within 4Å: Chain B: H.155, N.157, D.172, T.173, H.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.176 INS.6: 5 residues within 4Å: Chain C: H.155, N.157, D.172, T.173, H.176 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.157, C:D.172 Water bridges: C:Y.235 INS.8: 5 residues within 4Å: Chain D: H.155, N.157, D.172, T.173, H.176 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Straaten, K.E. et al., Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification. Biochem.J. (2010)

Release Date

2010-09-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

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

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