MolNFT v1 · #120158 · protein
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with MG(2+), citrate and ADP
5GRE · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with MG(2+), citrate and ADP”. X-ray diffraction, 2 ligands (ADP, MG), 6 pockets (best…
- PDB
- 5GRE
- Type
- protein
- Length
- 658 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
- ADP, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 325 | 45% helix, 22% strand | P50213 |
| B | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (EC 1.1.1.41) | protein | 333 | 42% helix, 21% strand | P51553 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.71 | 0.83 | 53 | ADP, MG, CIT |
| 2 | 510 | 0.70 | 0.80 | 45 | MG |
| 3 | 232 | 0.60 | 0.80 | 29 | empty |
| 4 | 253 | 0.56 | 0.77 | 25 | empty |
| 5 | 105 | 0.37 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2327 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5GRE · Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+)… · 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 0.98
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 5GRE · PDBe 5GRE · UniProt P50213 · UniProt P51553
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