Research workbench
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.
Analyse Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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