SMTL ID : 3nt4.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 23 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, E.96, K.97, G.124, M.126, H.176, Y.280 Ligands: INS.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:A.12, A:I.13, A:G.14, A:V.36, A:N.37, A:S.74, A:W.75, A:G.76, A:K.97, A:K.97, A:G.124 Water bridges: A:S.74, A:S.82, A:M.126 NAI.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, K.97, P.98, M.126, H.176, W.272, Y.280 Ligands: INS.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: 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:E.96, B:K.97 NAI.5: 23 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, E.96, K.97, G.124, M.126, H.176, Y.280 Ligands: INS.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:A.12, C:I.13, C:G.14, C:D.35, C:V.36, C:N.37, C:S.74, C:W.75, C:G.76, C:K.97, C:K.97, C:G.124, C:Y.280 Water bridges: C:S.74, C:S.82, C:M.126 NAI.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, K.97, P.98, M.126, H.176, W.272, Y.280 Ligands: INS.8 11 PLIP interactions: 11 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:S.74, D:W.75, D:E.96, D:K.97, D:Y.280

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

INS.2: 9 residues within 4Å: Chain A: K.97, H.155, N.157, D.172, T.173, H.176, Y.235, W.272 Ligands: NAI.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.97, A:K.97, A:H.155, A:N.157, A:H.176 Water bridges: A:Y.235 INS.4: 9 residues within 4Å: Chain B: K.97, H.155, N.157, D.172, T.173, H.176, Y.235, W.272 Ligands: NAI.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.97, B:K.97, B:H.155, B:N.157, B:N.157, B:H.176 Water bridges: B:R.127, B:W.272 INS.6: 9 residues within 4Å: Chain C: K.97, H.155, N.157, D.172, T.173, H.176, Y.235, W.272 Ligands: NAI.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.97, C:K.97, C:H.155, C:N.157, C:H.176, C:Y.235 Water bridges: C:R.127 INS.8: 9 residues within 4Å: Chain D: K.97, H.155, N.157, D.172, T.173, H.176, Y.235, W.272 Ligands: NAI.7 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.97, D:K.97, D:H.155, D:N.157, D:N.157, D:H.176, D:Y.235 Water bridges: D:R.127, 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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