MolNFT v1 · #154525 · protein
Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.
6KDY · Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: “Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.”. X-ray diffraction, 2 ligands (NAD, PE7), 20 pockets (best druggability 0.77). MolNFT…
- PDB
- 6KDY
- Type
- protein
- Length
- 2,697 residues
- Chains
- 8
- 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
- NAD, PE7
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 335 | 42% helix, 23% strand | P50213 |
| B, F, H | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 341 | 41% helix, 20% strand | O43837 |
| D | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial | protein | 342 | 43% helix, 22% strand | O43837 |
| E | Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) | protein | 327 | 43% helix, 22% strand | P50213 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- PE7 · 1-deoxy-1-thio-heptaethylene glycol · ligand · chains F
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, D
- 2PE · Nonaethylene glycol · additive · chains D
- P6G · Hexaethylene glycol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.77 | 0.91 | 44 | empty |
| 2 | 311 | 0.76 | 0.87 | 50 | empty |
| 3 | 93 | 0.75 | 0.96 | 21 | empty |
| 4 | 498 | 0.74 | 0.83 | 50 | NAD |
| 5 | 491 | 0.74 | 0.83 | 50 | NAD |
Interfaces
12 interfaces between chains.
- G–H · 2524 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2518 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2509 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2424 Ų buried · 45 hydrogen bonds · protein-protein
- F–H · 432 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6KDY · Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD. · the same entry in another collection · chain H against H, 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 0.97
- 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 0.95
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 6KDY · PDBe 6KDY · UniProt P50213 · UniProt O43837
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