Research workbench
Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with NAD+ and Mg2+
Analyse Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IXT
- Type
- protein
- Length
- 1,620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.78
- Source
- Ostreococcus tauri
- Molecule
- Isocitrate dehydrogenase
- UniProt
- A0A1Y5IEA9
- Ligands
- NAD, MG, SO4
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.78 · 1 distinct chain · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate dehydrogenase | protein | 405 | 44% helix, 23% strand | A0A1Y5IEA9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.67 | 0.77 | 62 | SO4 |
| 2 | 507 | 0.66 | 0.78 | 52 | GOL, SO4 |
| 3 | 579 | 0.64 | 0.76 | 56 | SO4 |
| 4 | 347 | 0.59 | 0.77 | 32 | empty |
| 5 | 386 | 0.57 | 0.75 | 49 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3186 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 3160 Ų buried · 63 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IXT · Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in complex with… · 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 A0A1Y5IEA9
- Elsewhere: RCSB PDB 6IXT · PDBe 6IXT · UniProt A0A1Y5IEA9
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