Research workbench
Human isocitrate dehydrogenase 1 bound with isocitrate
Analyse Human isocitrate dehydrogenase 1 bound with isocitrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFN
- Type
- protein
- Length
- 824 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
- ICT, MG, K
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 418 | 46% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 406 | 46% helix, 23% strand | O75874 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 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 | 816 | 0.74 | 0.78 | 79 | MG, ICT, K |
| 2 | 450 | 0.73 | 0.83 | 39 | MG, K, ICT |
| 3 | 275 | 0.58 | 0.78 | 38 | empty |
| 4 | 294 | 0.54 | 0.75 | 34 | empty |
| 5 | 255 | 0.51 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3558 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 5YFN · Human isocitrate dehydrogenase 1 bound with isocitrate · the same entry in another collection · chain A against A, TM-score 1.00
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 5YFN · PDBe 5YFN · UniProt O75874
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