Research workbench
Crystal structure of saccharomyces cerevesiae mitochondrial NADP(+)- dependent isocitrate dehydrogenase in complex with a-ketoglutarate
Analyse Crystal structure of saccharomyces cerevesiae mitochondrial NADP(+)- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QFY
- Type
- protein
- Length
- 2,466 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- P21954
- Ligands
- AKG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 411 | 47% helix, 22% strand | P21954 |
| B, C, E | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 411 | 46% helix, 22% strand | P21954 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.76 | 0.78 | 89 | empty |
| 2 | 926 | 0.76 | 0.78 | 86 | empty |
| 3 | 907 | 0.75 | 0.79 | 90 | AKG |
| 4 | 960 | 0.75 | 0.78 | 87 | AKG |
| 5 | 968 | 0.75 | 0.78 | 85 | AKG |
Interfaces
5 interfaces between chains.
- A–B · 3503 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 3479 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 3452 Ų buried · 53 hydrogen bonds · protein-protein
- B–F · 796 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 792 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2QFY · Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate… · the same entry in another collection · chain F against F, TM-score 1.00
- P21954 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P21954
- Elsewhere: RCSB PDB 2QFY · PDBe 2QFY · UniProt P21954
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