MolNFT v1 · #141196 · protein
Crystal structure of mouse cytosolic isocitrate dehydrogenase
5YZH · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of mouse cytosolic isocitrate dehydrogenase”. X-ray diffraction, 1 ligand (NAP), 8 pockets (best druggability 0.80). MolNFT v1 #141196 on GenesisL1: 3D structure…
- PDB
- 5YZH
- Type
- protein
- Length
- 821 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
- O88844
- Ligands
- NAP
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 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 | 412 | 48% helix, 22% strand | O88844 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 48% helix, 22% strand | O88844 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.80 | 0.82 | 91 | NAP |
| 2 | 912 | 0.79 | 0.81 | 75 | NAP |
| 3 | 92 | 0.49 | 0.82 | 19 | empty |
| 4 | 167 | 0.47 | 0.76 | 20 | empty |
| 5 | 183 | 0.46 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3963 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 5YZH · Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- O88844 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O88844) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O88844
- Elsewhere: RCSB PDB 5YZH · PDBe 5YZH · UniProt O88844
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