Research workbench
Crystal structure of isocitrate dehydrogenase from ostreococcus tauri
Analyse Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IXL
- Type
- protein
- Length
- 1,619 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- UniProt
- A0A1Y5IEA9
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Isocitrate dehydrogenase | protein | 405 | 44% helix, 22% strand | A0A1Y5IEA9 |
| D | Isocitrate dehydrogenase | protein | 404 | 45% helix, 24% strand | A0A1Y5IEA9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.68 | 0.77 | 63 | SO4 |
| 2 | 602 | 0.66 | 0.76 | 63 | SO4 |
| 3 | 534 | 0.63 | 0.76 | 57 | SO4 |
| 4 | 329 | 0.58 | 0.77 | 31 | empty |
| 5 | 332 | 0.58 | 0.76 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3185 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 3167 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IXL · Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri · 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 6IXL · PDBe 6IXL · UniProt A0A1Y5IEA9
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