Research workbench
Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and L-glucono-1,5-lactone, from paracoccus laeviglucosivorans
Analyse Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KTK
- Type
- protein
- Length
- 1,469 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
- NAI, 8S0
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 367 | 39% helix, 25% strand | K7ZP76 |
| B | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 366 | 39% helix, 25% strand | K7ZP76 |
| C, D | Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | protein | 368 | 38% helix, 24% strand | K7ZP76 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 8S0 · L-glucono-1,5-lactone · ligand · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, 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 | 1002 | 0.89 | 0.91 | 64 | empty |
| 2 | 69 | 0.76 | 0.99 | 19 | empty |
| 3 | 70 | 0.76 | 0.99 | 18 | empty |
| 4 | 603 | 0.66 | 0.76 | 75 | NAI, 8S0 |
| 5 | 503 | 0.66 | 0.78 | 58 | NAI, 8S0 |
Interfaces
6 interfaces between chains.
- A–B · 1875 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1862 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1807 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1772 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 817 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6KTK · Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NADH and… · 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 6KTK · PDBe 6KTK · UniProt K7ZP76
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