SMTL ID : 3nt5.1 (1 other biounit)

Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor and product inosose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: 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, K.97, G.124, M.126, Y.280 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.13 Hydrogen bonds: A:A.12, A:I.13, A:V.36, A:N.37, A:W.75, A:G.76, A:K.97, A:K.97, A:G.124 pi-Cation interactions: A:K.97 NAD.5: 19 residues within 4Å: Chain C: 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, K.97, G.124, M.126, Y.280 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.13 Hydrogen bonds: C:A.12, C:I.13, C:V.36, C:N.37, C:W.75, C:G.76, C:K.97, C:K.97, C:G.124, C:Y.280 pi-Cation interactions: C:K.97

4 x ISE: (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone(Non-covalent)

ISE.2: 7 residues within 4Å: Chain A: K.97, R.127, H.155, N.157, D.172, H.176, Y.235 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.97, A:K.97, A:R.127, A:N.157, A:H.176 ISE.4: 9 residues within 4Å: Chain B: K.97, R.127, H.155, N.157, D.172, H.176, Y.235, W.272 Ligands: NAI.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.97, B:K.97, B:R.127, B:N.157, B:H.176 ISE.6: 7 residues within 4Å: Chain C: K.97, R.127, H.155, N.157, D.172, H.176, Y.235 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.97, C:K.97, C:R.127, C:N.157, C:H.176, C:Y.235 ISE.8: 9 residues within 4Å: Chain D: K.97, R.127, H.155, N.157, D.172, H.176, Y.235, W.272 Ligands: NAI.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.97, D:K.97, D:R.127, D:N.157, D:H.176, D:Y.235

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 17 residues within 4Å: Chain B: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, D.58, S.74, W.75, A.78, H.79, S.82, K.97, W.272 Ligands: ISE.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.272 Hydrogen bonds: B:A.12, B:I.13, B:D.35, B:V.36, B:D.58, B:S.74, B:W.75, B:H.79, B:S.82, B:K.97, B:W.272 NAI.7: 17 residues within 4Å: Chain D: I.8, G.9, G.11, A.12, I.13, T.34, D.35, V.36, D.58, S.74, W.75, A.78, H.79, S.82, K.97, W.272 Ligands: ISE.8 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.272 Hydrogen bonds: D:A.12, D:I.13, D:D.35, D:V.36, D:D.58, D:S.74, D:W.75, D:H.79, D:S.82, D:K.97, D:W.272

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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