MolNFT v1 · #98135 · protein
Crystal structure analysis of human IDH1 mutants in complex with NADP+ and CA2+/ALPHA-ketoglutarate
4L06 · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure analysis of human IDH1 mutants in complex with NADP+ and CA2+/ALPHA-ketoglutarate”. X-ray diffraction, 3 ligands (NAP, AKG, CA), 20 pockets (best druggability 0.79).…
- PDB
- 4L06
- Type
- protein
- Length
- 2,472 residues
- Chains
- 6
- 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, AKG, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 413 | 48% helix, 23% strand | O75874 |
| B, F | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 49% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 48% helix, 23% strand | O75874 |
| D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 46% helix, 22% strand | O75874 |
Ligands and binding sites
- NAP · Nadp 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.79 | 0.81 | 84 | NAP, AKG |
| 2 | 990 | 0.79 | 0.80 | 84 | NAP, AKG |
| 3 | 962 | 0.78 | 0.81 | 84 | NAP, AKG |
| 4 | 899 | 0.78 | 0.81 | 69 | NAP, AKG |
| 5 | 961 | 0.78 | 0.80 | 79 | NAP, AKG |
Interfaces
7 interfaces between chains.
- E–F · 3771 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 3761 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3738 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 241 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4L06 · Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and… · 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 B against A, TM-score 0.97
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 4L06 · PDBe 4L06 · UniProt O75874
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.