SMTL ID : 7d5n.1

Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 24 residues within 4Å: Chain A: V.17, G.18, G.19, G.20, S.23, Q.24, I.25, A.45, F.46, D.47, I.48, A.91, T.92, P.93, N.94, H.97, E.114, K.115, T.141, A.187, W.190, R.191, H.209, W.333 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.25, A:I.25 Hydrogen bonds: A:G.18, A:G.19, A:G.20, A:Q.24, A:Q.24, A:I.25, A:I.48, A:T.92, A:N.94, A:E.114, A:K.115, A:T.141 Water bridges: A:N.22, A:S.23, A:D.47, A:G.143, A:G.143, A:R.191 Salt bridges: A:R.191 NAI.2: 26 residues within 4Å: Chain B: V.17, G.18, G.19, G.20, S.23, Q.24, I.25, A.45, F.46, D.47, I.48, A.91, T.92, P.93, N.94, H.97, E.114, K.115, P.116, T.141, A.187, W.190, R.191, H.209, W.333 Ligands: INS.3 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.25, B:I.25 Hydrogen bonds: B:G.18, B:G.19, B:G.20, B:Q.24, B:Q.24, B:I.25, B:I.48, B:T.92, B:N.94, B:E.114, B:K.115 Water bridges: B:N.22, B:S.23, B:S.23, B:G.26, B:D.47, B:G.143, B:G.143 Salt bridges: B:R.191 NAI.4: 24 residues within 4Å: Chain C: V.17, G.18, G.19, G.20, S.23, Q.24, I.25, A.45, F.46, D.47, I.48, A.91, T.92, P.93, N.94, H.97, E.114, K.115, T.141, A.187, W.190, R.191, H.209, W.333 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.25, C:I.25 Hydrogen bonds: C:G.18, C:G.19, C:G.20, C:Q.24, C:Q.24, C:I.25, C:I.48, C:T.92, C:N.94, C:E.114, C:K.115, C:T.141 Water bridges: C:N.22, C:S.23, C:D.47, C:G.143, C:G.143, C:R.191 Salt bridges: C:R.191 NAI.5: 26 residues within 4Å: Chain D: V.17, G.18, G.19, G.20, S.23, Q.24, I.25, A.45, F.46, D.47, I.48, A.91, T.92, P.93, N.94, H.97, E.114, K.115, P.116, T.141, A.187, W.190, R.191, H.209, W.333 Ligands: INS.6 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.25, D:I.25 Hydrogen bonds: D:G.18, D:G.19, D:G.20, D:Q.24, D:Q.24, D:I.25, D:I.48, D:T.92, D:N.94, D:E.114, D:K.115 Water bridges: D:N.22, D:S.23, D:S.23, D:G.26, D:D.47, D:G.143, D:G.143 Salt bridges: D:R.191

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

INS.3: 8 residues within 4Å: Chain A: H.325 Chain B: K.115, Y.144, F.172, R.191, D.205, H.209 Ligands: NAI.2 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.115, B:Y.144, B:Y.144, B:R.191, B:H.209 Water bridges: B:H.269, A:H.325 INS.6: 8 residues within 4Å: Chain C: H.325 Chain D: K.115, Y.144, F.172, R.191, D.205, H.209 Ligands: NAI.5 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.115, D:Y.144, D:Y.144, D:R.191, D:H.209 Water bridges: D:H.269, C:H.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukano, K. et al., Crystal structure of inositol dehydrogenase complexed with NADH and myo-inositol from Azotobacter vinelandii. To Be Published

Release Date

2021-09-29

Peptides

Oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Oxidoreductase