MolNFT v1 · #10220 · protein
Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7 ångströms resolution: conformational changes induced by decarboxylation of isocitrate
1IKA: “Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7 ångströms resolution: conformational…”. X-ray diffraction, 2 ligands (AKG, CA), 3 pockets (best druggability 0.62). MolNFT v1 #10220 on GenesisL1: 3D structure…
- PDB
- 1IKA
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- P08200
- Ligands
- AKG, CA
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 414 | 39% helix, 16% strand | P08200 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.62 | 0.76 | 45 | empty |
| 2 | 134 | 0.48 | 0.78 | 28 | empty |
| 3 | 83 | 0.31 | 0.73 | 21 | CA, AKG |
Compared structures
- 1IKA · Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7 ångströms… · the same entry in another collection · chain A against A, TM-score 1.00
- P08200 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P08200) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P08200
- Elsewhere: RCSB PDB 1IKA · PDBe 1IKA · UniProt P08200
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