MolNFT v1 · #67548 · protein
Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, alpha-ketoglutarate and CALCIUM(2+)
3INM · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with…”. X-ray diffraction, 4 ligands (NDP, AKG, CA), 10 pockets (best druggability…
- PDB
- 3INM
- Type
- protein
- Length
- 1,225 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- NDP, AKG, CA, NA
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 407 | 48% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 48% helix, 22% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.79 | 0.82 | 75 | NDP, AKG, CA |
| 2 | 899 | 0.79 | 0.82 | 70 | NDP, AKG, NA |
| 3 | 900 | 0.73 | 0.77 | 88 | empty |
| 4 | 323 | 0.55 | 0.76 | 55 | NDP, AKG, CA |
| 5 | 277 | 0.53 | 0.75 | 36 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 3948 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 321 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3INM · Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H… · the same entry in another collection · chain B against B, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O75874
- Elsewhere: RCSB PDB 3INM · PDBe 3INM · UniProt O75874
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