MolNFT v1 · #99945 · protein
Crystal structure of myo-inositol dehydrogenase from lactobacillus casei in complex with NAD and myo-inositol
4MIY · Inositol 2-DEHYDROGENASE/D-chiro-inositol 3-dehydrogenase: “Crystal structure of myo-inositol dehydrogenase from lactobacillus casei in complex with NAD and myo-inositol”. X-ray diffraction, 3 ligands (NAD, INS, SO4), 15 pockets…
- PDB
- 4MIY
- 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, INS, 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
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · chains D
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, C, B
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.88 | 0.89 | 124 | GOL |
| 2 | 409 | 0.69 | 0.81 | 43 | NAD, INS |
| 3 | 425 | 0.65 | 0.78 | 59 | NAD |
| 4 | 439 | 0.64 | 0.77 | 62 | NAD, GOL |
| 5 | 395 | 0.64 | 0.78 | 57 | NAD |
Interfaces
6 interfaces between chains.
- B–D · 1452 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1444 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1087 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1080 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4MIY · 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 4MIY · PDBe 4MIY · UniProt B3W8L3
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