Research workbench
Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from azotobacter vinelandii
Analyse Crystal structure of inositol dehydrogenase homolog complexed with NADH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D5N
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase
- UniProt
- C1DLC3
- Ligands
- NAI, INS
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 379 | 39% helix, 23% strand | C1DLC3 |
| B | Oxidoreductase | protein | 389 | 40% helix, 22% strand | C1DLC3 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.77 | 0.82 | 61 | NAI, INS |
| 2 | 543 | 0.74 | 0.82 | 58 | NAI |
| 3 | 332 | 0.67 | 0.81 | 36 | empty |
| 4 | 340 | 0.65 | 0.80 | 50 | empty |
| 5 | 270 | 0.63 | 0.81 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1712 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7D5N · Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol… · 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 C1DLC3
- Elsewhere: RCSB PDB 7D5N · PDBe 7D5N · UniProt C1DLC3
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