Research workbench
Crystal structure of K97V mutant of myo-inositol dehydrogenase from bacillus subtilis with bound cofactor NAD and inositol
Analyse Crystal structure of K97V mutant of myo-inositol dehydrogenase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NTR
- 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
- NAD, INS
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 39% 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 | 39% helix, 22% strand | P26935 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.67 | 0.79 | 57 | NAD, INS |
| 2 | 391 | 0.65 | 0.79 | 45 | NAD, INS |
| 3 | 259 | 0.63 | 0.81 | 37 | empty |
| 4 | 114 | 0.38 | 0.75 | 22 | empty |
| 5 | 73 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1428 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3NTR · Crystal structure of K97V mutant of myo-inositol dehydrogenase from Bacillus subtilis… · 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 3NTR · PDBe 3NTR · UniProt P26935
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