SMTL ID : 3mz0.1

Crystal structure of apo myo-inositol dehydrogenase from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-tetramer

Ligands

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: T.10, K.15, K.43, V.44, Q.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.15 PGE.2: 3 residues within 4Å: Chain A: L.84, K.88, E.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.88 PGE.9: 5 residues within 4Å: Chain B: T.10, K.15, K.43, V.44, Q.47 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.15 PGE.10: 3 residues within 4Å: Chain B: L.84, K.88, E.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.88 PGE.17: 5 residues within 4Å: Chain C: T.10, K.15, K.43, V.44, Q.47 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.15 PGE.18: 3 residues within 4Å: Chain C: L.84, K.88, E.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.88 PGE.25: 5 residues within 4Å: Chain D: T.10, K.15, K.43, V.44, Q.47 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.15 PGE.26: 3 residues within 4Å: Chain D: L.84, K.88, E.112 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.88

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.157, Y.164, T.173, W.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.173 GOL.11: 4 residues within 4Å: Chain B: N.157, Y.164, T.173, W.272 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.173 GOL.19: 4 residues within 4Å: Chain C: N.157, Y.164, T.173, W.272 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.173 GOL.27: 4 residues within 4Å: Chain D: N.157, Y.164, T.173, W.272 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.173

16 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: L.269, M.270, D.271, R.274 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: T.101 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: E.113, R.119, V.121, T.301, A.302, Y.336 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: K.330 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: L.269, M.270, D.271, R.274 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: T.101 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: E.113, R.119, V.121, T.301, A.302, Y.336 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: K.330 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain C: L.269, M.270, D.271, R.274 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain C: T.101 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain C: E.113, R.119, V.121, T.301, A.302, Y.336 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain C: K.330 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain D: L.269, M.270, D.271, R.274 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain D: T.101 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain D: E.113, R.119, V.121, T.301, A.302, Y.336 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain D: K.330 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 1 residues within 4Å: Chain A: D.267 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.267, H2O.4, H2O.6, H2O.6, H2O.7, H2O.12 MG.16: 1 residues within 4Å: Chain B: D.267 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.267, H2O.19, H2O.20, H2O.21, H2O.22, H2O.26 MG.24: 1 residues within 4Å: Chain C: D.267 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.267, H2O.33, H2O.34, H2O.35, H2O.36, H2O.41 MG.32: 1 residues within 4Å: Chain D: D.267 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.267, H2O.47, H2O.49, H2O.49, H2O.50, H2O.55

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

2010-09-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

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

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