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

X-ray diffraction
2.901Å resolution
PDB entry 3nt5 coloured by chain, front view.
PDB entry 3nt5 coloured by chain, side view.
PDB entry 3nt5 coloured by chain, top view.
Source organism: Bacillus subtilis
Assemblies composition:
homo tetramer (preferred)
homo hexamer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
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Multimeric state: homo tetramer
Accessible surface area: 50265.95 Å2
Buried surface area: 16704.19 Å2
Dissociation area: 3,464.11 Å2
Dissociation energy (ΔGdiss): 39.75 kcal/mol
Dissociation entropy (TΔSdiss): 15.74 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-150888
Homo tetrameric assembly 1 of PDB entry 3nt5 coloured by chemically distinct molecules, front view.
Homo tetrameric assembly 1 of PDB entry 3nt5 coloured by chemically distinct molecules, side view.
Homo tetrameric assembly 1 of PDB entry 3nt5 coloured by chemically distinct molecules, top view.
    Assembly 1
Confidence : 98%
No. subunits : 4
Symmetry : D2
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3DComplex & QSbio predictionx
No. subunits : 4
Symmetry : D2
Evidence : Interface geometry is similar to that of 4mkx_1 (26% id)
Assembly 2
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Assembly Name: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
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Multimeric state: homo hexamer
Accessible surface area: 83152.77 Å2
Buried surface area: 17316.64 Å2
Dissociation area: 5,369.84 Å2
Dissociation energy (ΔGdiss): 20.68 kcal/mol
Dissociation entropy (TΔSdiss): 71.65 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-150889
Homo hexameric assembly 2 of PDB entry 3nt5 coloured by chemically distinct molecules, front view.
Homo hexameric assembly 2 of PDB entry 3nt5 coloured by chemically distinct molecules, side view.
Homo hexameric assembly 2 of PDB entry 3nt5 coloured by chemically distinct molecules, top view.
    Assembly 2
Confidence : 0%
No. subunits : 6
Symmetry : C3
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3DComplex & QSbio predictionx
No. subunits : 4
Symmetry : D2
Evidence : Sequence is/are identical to 4l8v_1 (which is supposedly correct) but the structure is different, and the stoichiometry appears inconsistent with the composition and/or symmetry

Macromolecules

Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
Chains: A, B
Length: 344 amino acids
Theoretical weight: 38.39 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P26935 (Residues: 1-344; Coverage: 100%)
Gene names: BSU39700, E83G, idh, iolG
Pfam:
InterPro:
CATH:
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase in PDB entry 3nt5, assembly 1, front view.
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase in PDB entry 3nt5, assembly 1, side view.
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase in PDB entry 3nt5, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P26935  
134450100150200250300
 
100200300
UniProt
P26935
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Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
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