Research workbench
Crystal structure of myo-inositol dehydrogenase from lactobacillus casei in complex with NAD and D-chiro-inositol
Analyse Crystal structure of myo-inositol dehydrogenase from lactobacillus casei in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MJL
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- 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
- B3W8L3
- Ligands
- NAD, CBU, SO4
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Inositol 2-DEHYDROGENASE/D-chiro-inositol 3-dehydrogenase (EC 1.1.1.18) | protein | 339 | 37% helix, 23% strand | B3W8L3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CBU · (1R,2R,3S,4S,5S,6S)-cyclohexane-1,2,3,4,5,6-hexol · ligand · chains D
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, C, B
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.88 | 0.91 | 101 | GOL |
| 2 | 329 | 0.68 | 0.82 | 34 | NAD, CBU |
| 3 | 456 | 0.66 | 0.78 | 64 | NAD |
| 4 | 375 | 0.64 | 0.79 | 45 | NAD |
| 5 | 338 | 0.62 | 0.79 | 47 | NAD |
Interfaces
6 interfaces between chains.
- B–D · 1461 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1449 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1099 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1097 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 712 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4MJL · Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with… · the same entry in another collection · 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 B3W8L3
- Elsewhere: RCSB PDB 4MJL · PDBe 4MJL · UniProt B3W8L3
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