Research workbench
Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.
Analyse Crystal structure of the alpha bata heterodimer of human IDH3 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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