SMTL ID : 4mie.1

Crystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: H.167, D.184, T.185, H.188, Y.248, W.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.185, A:H.188, A:Y.248 GOL.2: 8 residues within 4Å: Chain A: R.164, A.165, S.166, K.251, E.253 Chain C: R.164, E.253 Ligands: GOL.11 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.166, A:S.166, A:E.253, A:E.253, C:R.164, C:R.164 GOL.3: 7 residues within 4Å: Chain A: I.20, T.46, D.47, I.48, P.68, D.69, D.70 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.46, A:D.70, A:D.70 Water bridges: A:I.48, A:S.86, A:A.90, A:T.94, A:T.94 GOL.5: 6 residues within 4Å: Chain A: I.271, Q.278 Chain B: I.271, Q.278, Q.279, T.280 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.278, B:T.280, A:Q.278 GOL.6: 1 residues within 4Å: Chain B: L.37 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Water bridges: B:N.295, B:T.296, B:Q.299, C:N.295 GOL.7: 8 residues within 4Å: Chain B: R.164, A.165, S.166, K.251, E.253 Chain D: R.164, E.253 Ligands: GOL.14 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:R.164, D:R.164, B:S.166, B:E.253, B:E.253 GOL.8: 7 residues within 4Å: Chain B: H.167, N.169, D.184, T.185, H.188, Y.248, W.286 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.185, B:H.188 Water bridges: B:Y.248 GOL.10: 6 residues within 4Å: Chain C: H.167, D.184, T.185, H.188, Y.248, W.286 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.248 Water bridges: C:D.184, C:H.188 GOL.11: 8 residues within 4Å: Chain A: R.164, E.253 Chain C: R.164, A.165, S.166, K.251, E.253 Ligands: GOL.2 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.166, C:S.166, A:R.164, A:E.253 GOL.14: 8 residues within 4Å: Chain B: R.164, E.253 Chain D: R.164, A.165, S.166, K.251, E.253 Ligands: GOL.7 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.164, D:E.253, B:R.164, B:E.253 Water bridges: D:S.166 GOL.15: 8 residues within 4Å: Chain D: K.109, M.138, H.167, D.184, T.185, H.188, Y.248, W.286 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.188 Water bridges: D:Y.248 GOL.16: 6 residues within 4Å: Chain D: R.140, Y.141, R.146, E.300, V.312 Ligands: SO4.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.146, D:R.146 Water bridges: D:R.146

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

SO4.4: 1 residues within 4Å: Chain A: R.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.120 SO4.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 4 residues within 4Å: Chain A: A.159, P.160, K.232 Chain C: R.210 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.210, A:K.232 SO4.13: 4 residues within 4Å: Chain B: T.38, G.39 Chain C: T.38, G.39 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.39, C:T.38, C:G.39 Water bridges: B:T.38 SO4.17: 3 residues within 4Å: Chain D: R.146, W.195 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.146 SO4.18: 5 residues within 4Å: Chain A: T.38, G.39 Chain D: H.10, T.38, G.39 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:G.39, A:G.39 Water bridges: D:A.40, D:A.40, A:A.40, A:A.40, A:A.40 Salt bridges: D:H.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertwistle, D. et al., Crystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei. 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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