Research workbench
Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate
Analyse Crystal structure of homodimeric R132H mutant of human cytosolic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MAP
- Type
- protein
- Length
- 795 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- NAP, ICT
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 397 | 45% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 398 | 45% helix, 23% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ICT · Isocitric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.82 | 0.85 | 75 | empty |
| 2 | 259 | 0.67 | 0.83 | 36 | empty |
| 3 | 349 | 0.65 | 0.80 | 44 | NAP, ICT |
| 4 | 229 | 0.56 | 0.78 | 34 | empty |
| 5 | 205 | 0.55 | 0.79 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2445 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 3MAP · 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 0.92
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 3MAP · PDBe 3MAP · UniProt O75874
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