MolNFT v1 · #141087 · protein
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with MG(2+) and NADH
5YVT · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with MG(2+) and NADH”. X-ray diffraction, 2 ligands (NAI, MG), 7 pockets (best druggability…
- PDB
- 5YVT
- Type
- protein
- Length
- 665 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
- NAI, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 332 | 40% helix, 24% strand | P50213 |
| B | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial | protein | 333 | 41% helix, 23% strand | P51553 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.71 | 0.99 | 19 | empty |
| 2 | 625 | 0.71 | 0.79 | 51 | MG |
| 3 | 360 | 0.69 | 0.82 | 56 | NAI |
| 4 | 235 | 0.59 | 0.79 | 34 | empty |
| 5 | 307 | 0.58 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2439 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5YVT · Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and… · 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 5YVT · PDBe 5YVT · UniProt P50213 · UniProt P51553
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