MolNFT v1 · #155364 · protein
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with cit, mg and ATP binding at allosteric site and mg, ATP binding at active site.
6L59 · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with cit, mg and ATP binding at…”. X-ray diffraction, 2 ligands (ATP, MG), 5 pockets (best…
- PDB
- 6L59
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial; Isocitrate dehydrogenase…
- EC
- 1.1.1.41
- UniProt
- P50213, P51553
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 325 | 44% helix, 22% strand | P50213 |
| B | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial | protein | 331 | 42% helix, 21% strand | P51553 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.70 | 0.83 | 51 | ATP, MG, CIT |
| 2 | 467 | 0.66 | 0.78 | 41 | MG |
| 3 | 199 | 0.61 | 0.82 | 27 | empty |
| 4 | 258 | 0.57 | 0.77 | 25 | empty |
| 5 | 63 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2259 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6L59 · Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT, Mg… · the same entry in another collection · chain A against A, TM-score 1.00
- P51553 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit gamma… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P50213 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P50213
- Every structure of UniProt P51553
- Elsewhere: RCSB PDB 6L59 · PDBe 6L59 · UniProt P50213 · UniProt P51553
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