Research workbench
Cryo-EM structure of isocitrate dehydrogenase (IDH1)
Analyse Cryo-EM structure of isocitrate dehydrogenase (IDH1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K10
- Type
- protein
- Length
- 794 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- NDP
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 397 | 41% helix, 19% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.79 | 0.86 | 71 | empty |
| 2 | 132 | 0.63 | 0.86 | 31 | empty |
| 3 | 115 | 0.61 | 0.86 | 24 | empty |
| 4 | 58 | 0.50 | 0.87 | 20 | empty |
| 5 | 159 | 0.47 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2451 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5K10 · Cryo-EM structure of isocitrate dehydrogenase (IDH1) · the same entry in another collection · chain A against A, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 O75874
- Elsewhere: RCSB PDB 5K10 · PDBe 5K10 · UniProt O75874
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