Research workbench
Crystal structure of human mitochondrial isocitrate dehydrogenase R140Q mutant homodimer bound to NADPH and alpha-ketoglutaric acid
Analyse Crystal structure of human mitochondrial isocitrate dehydrogenase R140Q mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I95
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP], mitochondrial
- EC
- 1.1.1.42
- UniProt
- P48735
- Ligands
- NDP, AKG, CA
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 413 | 46% helix, 19% strand | P48735 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.51 | 0.75 | 35 | CA, AKG |
| 2 | 192 | 0.49 | 0.76 | 20 | GOL |
| 3 | 147 | 0.42 | 0.75 | 27 | ACT |
| 4 | 50 | 0.28 | 0.74 | 14 | empty |
Compared structures
- 5I95 · Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer… · the same entry in another collection · chain A against A, TM-score 1.00
- P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain A 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 P48735
- Elsewhere: RCSB PDB 5I95 · PDBe 5I95 · UniProt P48735
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