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Crystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei
Analyse Crystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MIE
- Type
- protein
- Length
- 1,361 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Lactobacillus casei
- Molecule
- Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
- EC
- 1.1.1.18
- UniProt
- B3W8L3
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase (EC 1.1.1.18) | protein | 339 | 38% helix, 23% strand | B3W8L3 |
| D | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase (EC 1.1.1.18) | protein | 344 | 36% helix, 23% strand | B3W8L3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 12 copies · chains A, C, B, 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 | 439 | 0.84 | 0.91 | 71 | GOL |
| 2 | 362 | 0.82 | 0.92 | 63 | GOL |
| 3 | 300 | 0.65 | 0.81 | 31 | GOL |
| 4 | 377 | 0.65 | 0.79 | 48 | GOL |
| 5 | 367 | 0.65 | 0.79 | 49 | GOL |
Interfaces
6 interfaces between chains.
- A–C · 1460 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1454 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1136 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1112 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 720 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4MIE · Crystal structure of apo myo-inositol dehydrogenase from lactobacillus casei · 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 4MIE · PDBe 4MIE · UniProt B3W8L3
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