Research workbench
Crystal structure of myo-inositol dehydrogenase from bacillus subtilis with bound cofactor and product inosose
Analyse Crystal structure of myo-inositol dehydrogenase from bacillus subtilis with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NT5
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol 2-DEHYDROGENASE/D-chiro-inositol 3-dehydrogenase
- EC
- 1.1.1.18
- UniProt
- P26935
- Ligands
- ISE, NAD, NAI
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inositol 2-DEHYDROGENASE/D-chiro-inositol 3-dehydrogenase (EC 1.1.1.18) | protein | 337 | 37% helix, 22% strand | P26935 |
Ligands and binding sites
- ISE · (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.61 | 0.78 | 30 | NAD, ISE |
| 2 | 242 | 0.61 | 0.81 | 37 | empty |
| 3 | 291 | 0.60 | 0.78 | 29 | NAI, ISE |
| 4 | 71 | 0.52 | 0.85 | 18 | empty |
| 5 | 65 | 0.49 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1424 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3NT5 · Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P26935 · AlphaFold monomer V2.0 prediction for inositol 2-DEHYDROGENASE/D-chiro-inositol… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P26935
- Elsewhere: RCSB PDB 3NT5 · PDBe 3NT5 · UniProt P26935
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