MolNFT v1 · #71318 · protein
Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP
3MAR · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase…”. X-ray diffraction, 1 ligand (NAP), 9 pockets (best druggability 0.71).…
- PDB
- 3MAR
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- 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
- NAP
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 393 | 41% helix, 17% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 395 | 45% helix, 21% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.71 | 0.78 | 76 | NAP |
| 2 | 552 | 0.62 | 0.75 | 46 | empty |
| 3 | 158 | 0.62 | 0.84 | 26 | empty |
| 4 | 253 | 0.60 | 0.79 | 28 | empty |
| 5 | 250 | 0.59 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2231 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 3MAR · Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent… · the same entry in another collection · chain A against A, 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 0.91
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 3MAR · PDBe 3MAR · UniProt O75874
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