MolNFT v1 · #49172 · protein
Crystal structure of saccharomyces cerevesiae mitochondrial NADP(+)- dependent isocitrate dehydrogenase in complex with NADPH, a- ketoglutarate and CA(2+)
2QFX · Isocitrate dehydrogenase [NADP]: “Crystal structure of saccharomyces cerevesiae mitochondrial NADP(+)- dependent isocitrate dehydrogenase in…”. X-ray diffraction, 3 ligands (NDP, AKG, CA), 20 pockets (best druggability 0.81). MolNFT…
- PDB
- 2QFX
- Type
- protein
- Length
- 2,460 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
- NDP, AKG, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 410 | 45% helix, 23% strand | P21954 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.81 | 0.82 | 89 | CA, NDP, AKG |
| 2 | 1019 | 0.80 | 0.82 | 86 | CA, NDP, AKG |
| 3 | 865 | 0.80 | 0.83 | 70 | CA, NDP, AKG |
| 4 | 809 | 0.80 | 0.83 | 70 | CA, NDP, AKG |
| 5 | 805 | 0.79 | 0.82 | 63 | NDP, AKG |
Interfaces
5 interfaces between chains.
- E–F · 4043 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 4006 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 4005 Ų buried · 66 hydrogen bonds · protein-protein
- A–E · 594 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 583 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2QFX · Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate… · the same entry in another collection · chain C against C, 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 0.98
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 2QFX · PDBe 2QFX · UniProt P21954
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