MolNFT v1 · #120161 · protein
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with MG(2+)
5GRH · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with MG(2+)”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5GRH
- Type
- protein
- Length
- 662 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
- MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 327 | 45% helix, 23% strand | P50213 |
| B | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (EC 1.1.1.41) | protein | 335 | 43% helix, 23% strand | P51553 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.73 | 0.98 | 15 | empty |
| 2 | 342 | 0.73 | 0.85 | 49 | empty |
| 3 | 507 | 0.68 | 0.79 | 47 | MG |
| 4 | 312 | 0.60 | 0.78 | 34 | empty |
| 5 | 217 | 0.60 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2336 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5GRH · 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 0.98
- 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 5GRH · PDBe 5GRH · UniProt P50213 · UniProt P51553
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