Research workbench
Crystal structure of scyllo-inositol dehydrogenase from lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol
Analyse Crystal structure of scyllo-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
- 4N54
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol dehydrogenase
- EC
- 1.1.1.-
- UniProt
- B3W8L4
- Ligands
- NAI, 2H3
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Inositol dehydrogenase (EC 1.1.1.-) | protein | 340 | 42% helix, 26% strand | B3W8L4 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 2H3 · (1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol · ligand · 3 copies · chains A, B, 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 | 339 | 0.87 | 0.96 | 33 | empty |
| 2 | 354 | 0.76 | 0.86 | 41 | NAI, 2H3 |
| 3 | 392 | 0.76 | 0.85 | 46 | NAI, 2H3 |
| 4 | 544 | 0.73 | 0.81 | 53 | NAI, 2H3 |
| 5 | 536 | 0.71 | 0.79 | 54 | NAI |
Interfaces
6 interfaces between chains.
- B–D · 1796 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1790 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1230 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1206 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 605 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4N54 · Crystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound… · 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 B3W8L4
- Elsewhere: RCSB PDB 4N54 · PDBe 4N54 · UniProt B3W8L4
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