MolNFT v1 · #120159 · protein
Crystal structure of the alpha gamma mutant (gamma-K151A) of human IDH3 in complex with MG(2+), citrate and ADP
5GRF · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha gamma mutant (gamma-K151A) of human IDH3 in complex with MG(2+), citrate and…”. X-ray diffraction, 2 ligands (ADP, MG), 8 pockets (best…
- PDB
- 5GRF
- Type
- protein
- Length
- 659 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
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 324 | 42% helix, 24% strand | P50213 |
| B | Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (EC 1.1.1.41) | protein | 335 | 43% helix, 22% strand | P51553 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.80 | 0.98 | 32 | empty |
| 2 | 360 | 0.71 | 0.83 | 59 | CIT, ADP, MG |
| 3 | 445 | 0.67 | 0.79 | 40 | empty |
| 4 | 239 | 0.61 | 0.81 | 34 | empty |
| 5 | 290 | 0.58 | 0.77 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2331 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 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 5GRF · PDBe 5GRF · UniProt P50213 · UniProt P51553
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