Research workbench
Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with scyllo-inosose
Analyse Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YAQ
- Type
- protein
- Length
- 1,460 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, ISE
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 366 | 39% helix, 25% strand | K7ZP76 |
| D | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 362 | 38% helix, 23% strand | K7ZP76 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ISE · (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.89 | 0.91 | 66 | empty |
| 2 | 60 | 0.75 | 0.99 | 16 | empty |
| 3 | 57 | 0.74 | 1.00 | 15 | empty |
| 4 | 578 | 0.69 | 0.78 | 73 | NAD, ISE |
| 5 | 557 | 0.69 | 0.78 | 75 | NAD |
Interfaces
6 interfaces between chains.
- A–B · 1872 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1867 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 1751 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 1740 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 850 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5YAQ · 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 5YAQ · PDBe 5YAQ · UniProt K7ZP76
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