MolNFT v1 · #154507 · protein
Crystal structure of the alpha beta heterodimer of human IDH3 in complex with CA(2+)
6KDE · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha beta heterodimer of human IDH3 in complex with CA(2+)”. X-ray diffraction, 1 ligand (CA), 16 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 6KDE
- Type
- protein
- Length
- 1,304 residues
- Chains
- 4
- 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, O43837
- Ligands
- CA
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 336 | 41% helix, 21% strand | P50213 |
| B, D | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 316 | 44% helix, 22% strand | O43837 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.72 | 0.80 | 53 | CA |
| 2 | 656 | 0.72 | 0.79 | 62 | CA |
| 3 | 414 | 0.71 | 0.82 | 51 | empty |
| 4 | 325 | 0.69 | 0.83 | 37 | empty |
| 5 | 255 | 0.60 | 0.79 | 31 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2211 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2183 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 322 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 318 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 171 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6KDE · Crystal structure of the alpha beta heterodimer of human IDH3 in complex with Ca(2+) · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- O43837 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NAD] subunit beta… · a predicted model of the same protein · chain B 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 O43837
- Elsewhere: RCSB PDB 6KDE · PDBe 6KDE · UniProt P50213 · UniProt O43837
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