MolNFT v1 · #23382 · protein
Isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix in complex with etheno-NADP
1TYO: “Isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix in complex with etheno-NADP”. X-ray diffraction, 1 ligand (ENP), 4 pockets (best druggability 0.74). MolNFT v1 #23382 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1TYO
- Type
- protein
- Length
- 851 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- Q9YE81
- Ligands
- ENP
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 427 | 46% helix, 19% strand | Q9YE81 |
| B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 424 | 46% helix, 18% strand | Q9YE81 |
Ligands and binding sites
- ENP · Etheno-nadp · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.74 | 0.79 | 83 | empty |
| 2 | 927 | 0.74 | 0.78 | 86 | empty |
| 3 | 158 | 0.57 | 0.81 | 24 | empty |
| 4 | 73 | 0.46 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2993 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1TYO · Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix 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 Q9YE81
- Elsewhere: RCSB PDB 1TYO · PDBe 1TYO · UniProt Q9YE81
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