Research workbench
Human isocitrate dehydrogenase 1 bound with NADP
Analyse Human isocitrate dehydrogenase 1 bound with NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFM
- Type
- protein
- Length
- 1,226 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, MG
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 48% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 408 | 48% helix, 21% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.67 | 0.76 | 80 | NAP, MG |
| 2 | 466 | 0.60 | 0.75 | 48 | MG |
| 3 | 234 | 0.57 | 0.78 | 35 | empty |
| 4 | 237 | 0.56 | 0.78 | 34 | empty |
| 5 | 240 | 0.55 | 0.77 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3148 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 231 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YFM · Human isocitrate dehydrogenase 1 bound with NADP · 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 5YFM · PDBe 5YFM · UniProt O75874
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