MolNFT v1 · #98118 · protein
Crystal structure analysis of human IDH1 mutants in complex with NADP+ and CA2+/ALPHA-ketoglutarate
4KZO · 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), 12 pockets (best druggability 0.78).…
- PDB
- 4KZO
- Type
- protein
- Length
- 1,236 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
- NAP, AKG, CA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 414 | 48% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 48% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 410 | 48% helix, 21% strand | O75874 |
Ligands and binding sites
- NAP · Nadp 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
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.78 | 0.81 | 78 | NAP, AKG |
| 2 | 838 | 0.77 | 0.81 | 74 | CA, NAP, AKG |
| 3 | 845 | 0.73 | 0.78 | 75 | empty |
| 4 | 219 | 0.50 | 0.76 | 32 | empty |
| 5 | 205 | 0.49 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3760 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4KZO · Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and… · 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 B 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 4KZO · PDBe 4KZO · UniProt O75874
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