SMTL ID : 3ntq.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, T.73, 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 Chain E: E.39, Q.42 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:W.272, A:W.272 Hydrogen bonds: A:A.12, A:I.13, A:G.14, A:D.35, A:V.36, A:S.74, A:W.75, A:G.124, E:E.39, E:Q.42 Water bridges: A:G.11, A:D.58, A:S.82 NAD.2: 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, B:W.272 Hydrogen bonds: B:A.12, B:I.13, B:D.35, B:V.36, B:N.37, B:S.74, B:S.74, B:W.75, B:A.78, B:E.96 Water bridges: B:G.11, B:G.14 NAD.3: 24 residues within 4Å: Chain A: E.39, Q.42 Chain C: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, T.73, 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 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:W.272, C:W.272 Hydrogen bonds: C:A.12, C:I.13, C:G.14, C:V.36, C:S.74, C:W.75, C:G.124, A:E.39, A:E.39, A:Q.42 Water bridges: C:G.11, C:D.58, C:S.82 NAD.4: 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 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:W.272, D:W.272 Hydrogen bonds: D:A.12, D:I.13, D:D.35, D:V.36, D:N.37, D:S.74, D:S.74, D:W.75, D:A.78, D:E.96, D:Y.280 Water bridges: D:G.11, D:G.14 NAD.5: 24 residues within 4Å: Chain C: E.39, Q.42 Chain E: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, T.73, 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 16 PLIP interactions: 13 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:W.272, E:W.272 Hydrogen bonds: E:A.12, E:I.13, E:G.14, E:D.35, E:V.36, E:S.74, E:W.75, E:G.124, C:E.39, C:E.39, C:Q.42 Water bridges: E:G.11, E:D.58, E:S.82 NAD.6: 22 residues within 4Å: Chain F: 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 F Hydrophobic interactions: F:W.272, F:W.272 Hydrogen bonds: F:A.12, F:I.13, F:V.36, F:N.37, F:S.74, F:S.74, F:W.75, F:A.78, F:E.96, F:Y.280 Water bridges: F:G.11, F:G.14

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

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

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