MolNFT v1 · #152916 · protein
Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in complex with NAD+ and citrate
6IXN: “Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in complex with NAD+ and citrate”. X-ray diffraction, 2 ligands (NAD, SO4), 18 pockets (best druggability 0.77). MolNFT v1 #152916 on GenesisL1: 3D structure…
- PDB
- 6IXN
- Type
- protein
- Length
- 1,620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- UniProt
- A0A1Y5IEA9
- Ligands
- NAD, SO4
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate dehydrogenase | protein | 405 | 46% helix, 24% strand | A0A1Y5IEA9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.77 | 0.80 | 88 | FLC, NAD, GOL |
| 2 | 824 | 0.77 | 0.81 | 57 | FLC, NAD |
| 3 | 830 | 0.77 | 0.81 | 64 | FLC, NAD |
| 4 | 781 | 0.76 | 0.80 | 59 | FLC, NAD |
| 5 | 282 | 0.50 | 0.74 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3786 Ų buried · 81 hydrogen bonds · protein-protein
- A–B · 3762 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 278 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6IXN · 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 6IXN · PDBe 6IXN · UniProt A0A1Y5IEA9
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