MolNFT v1 · #140420 · protein
Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol
5YA8: “Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with…”. X-ray diffraction, 2 ligands (NAD, INS), 14 pockets (best druggability 0.89). MolNFT v1 #140420 on GenesisL1: 3D structure…
- PDB
- 5YA8
- Type
- protein
- Length
- 1,463 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
- UniProt
- K7ZP76
- Ligands
- NAD, INS
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 366 | 38% helix, 25% strand | K7ZP76 |
| D | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 365 | 38% helix, 23% strand | K7ZP76 |
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 · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.89 | 0.91 | 64 | empty |
| 2 | 64 | 0.75 | 0.99 | 17 | empty |
| 3 | 54 | 0.74 | 1.00 | 16 | empty |
| 4 | 485 | 0.70 | 0.80 | 70 | NAD, INS |
| 5 | 553 | 0.69 | 0.79 | 62 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1877 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1854 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1775 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 1756 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 834 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5YA8 · Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity… · 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 K7ZP76
- Elsewhere: RCSB PDB 5YA8 · PDBe 5YA8 · UniProt K7ZP76
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