SMTL ID : 4mjl.1

Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD and D-chiro-inositol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 20 residues within 4Å: Chain A: G.21, T.22, G.23, A.24, M.25, D.47, I.48, V.85, S.86, F.87, G.88, A.90, H.91, E.108, K.109, G.136, M.138, H.188, W.286, Y.294 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:M.25, A:W.286, A:W.286 Hydrogen bonds: A:A.24, A:M.25, A:I.48, A:D.49, A:S.86, A:F.87, A:E.108, A:Y.294 Water bridges: A:G.23, A:G.26, A:D.70, A:D.70, A:D.70, A:S.86, A:S.86, A:T.94, A:T.94 pi-Stacking: A:F.87 NAD.6: 22 residues within 4Å: Chain B: I.20, G.21, T.22, G.23, A.24, M.25, D.47, I.48, V.85, S.86, F.87, G.88, A.90, H.91, E.108, K.109, P.110, G.136, M.138, H.188, W.286, Y.294 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.286 Hydrogen bonds: B:A.24, B:M.25, B:G.26, B:I.48, B:S.86, B:F.87, B:E.108 Water bridges: B:G.23, B:D.70, B:S.86, B:S.86, B:G.88, B:G.88, B:T.94 pi-Stacking: B:F.87 NAD.10: 20 residues within 4Å: Chain C: G.21, T.22, G.23, A.24, M.25, D.47, I.48, V.85, S.86, F.87, G.88, A.90, H.91, E.108, K.109, P.110, G.136, M.138, H.188, Y.294 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:A.24, C:M.25, C:I.48, C:S.86, C:F.87, C:E.108, C:Y.294 Water bridges: C:G.23, C:G.26, C:S.86, C:S.86, C:K.109, C:D.184 pi-Stacking: C:F.87 NAD.15: 23 residues within 4Å: Chain D: I.20, G.21, T.22, G.23, A.24, M.25, D.47, I.48, V.85, S.86, F.87, G.88, A.90, H.91, E.108, K.109, G.136, M.138, D.184, H.188, W.286, Y.294 Ligands: CBU.16 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:M.25 Hydrogen bonds: D:G.23, D:A.24, D:M.25, D:G.26, D:I.48, D:S.86, D:F.87, D:E.108, D:K.109, D:D.184 Water bridges: D:S.86, D:G.88, D:T.94, D:T.94, D:N.175, D:N.175, D:N.175, D:N.175 pi-Stacking: D:W.286, D:W.286

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: I.271, Q.278, Q.279, T.280 Chain B: Q.278, Q.279, T.280 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.278, B:T.280, B:T.280, A:Q.278 GOL.3: 9 residues within 4Å: Chain A: R.164, E.253 Chain C: R.164, A.165, S.166, K.251, L.252, E.253 Ligands: GOL.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.164, A:R.164, C:S.166 Water bridges: C:S.166 GOL.7: 5 residues within 4Å: Chain B: L.152, D.153, G.158, A.159, P.160 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.153, B:D.153 Water bridges: D:R.210 GOL.11: 8 residues within 4Å: Chain C: I.271, Q.278, Q.279, T.280 Chain D: I.271, Q.278, Q.279, T.280 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.278, C:T.280, D:Q.278 GOL.12: 3 residues within 4Å: Chain B: V.36 Chain C: V.36, L.37 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.295 GOL.13: 9 residues within 4Å: Chain A: R.164, A.165, S.166, K.251, L.252, E.253 Chain C: R.164, E.253 Ligands: GOL.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.164, A:S.166, A:E.253, C:R.164, C:E.253 Water bridges: A:L.252 GOL.17: 7 residues within 4Å: Chain D: L.74, Q.75, D.76, P.77, T.101, D.102, K.103 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.74, D:D.102, D:K.103, D:K.103 GOL.18: 6 residues within 4Å: Chain D: R.140, Y.141, R.146, E.300, V.312 Ligands: SO4.19 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.141, D:R.146, D:V.312

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: T.38, G.39 Chain D: T.38, G.39 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.39, D:G.39 Water bridges: D:A.40, D:A.40 SO4.5: 4 residues within 4Å: Chain A: R.210 Chain C: A.159, P.160, K.232 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:R.210 Salt bridges: A:R.210, C:K.232 SO4.8: 4 residues within 4Å: Chain B: R.210 Chain D: A.159, P.160, K.232 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.210, D:K.232 SO4.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.14: 4 residues within 4Å: Chain A: A.159, P.160, K.232 Chain C: R.210 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:R.210, C:R.210 Salt bridges: C:R.210, A:K.232 SO4.19: 3 residues within 4Å: Chain D: R.146, W.195 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.195 Salt bridges: D:R.146

1 x CBU: (1R,2R,3S,4S,5S,6S)-CYCLOHEXANE-1,2,3,4,5,6-HEXOL

CBU.16: 10 residues within 4Å: Chain D: K.109, H.167, N.169, Y.176, D.184, T.185, H.188, Y.248, W.286 Ligands: NAD.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.169, D:N.169, D:N.169, D:T.185, D:H.188, D:Y.248, D:W.286 Water bridges: D:R.139, D:Y.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertwistle, D. et al., Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD and D-chiro-inositol. To be Published

Release Date

2015-03-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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