MolNFT v1 · #120538 · protein
Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate
5H3F · Isocitrate dehydrogenase [NADP], mitochondrial: “Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate”. X-ray diffraction, 2 ligands (ICT, MG), 9 pockets (best druggability 0.75). MolNFT v1 #120538 on…
- PDB
- 5H3F
- Type
- protein
- Length
- 832 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP], mitochondrial
- EC
- 1.1.1.42
- UniProt
- P54071
- Ligands
- ICT, MG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 415 | 46% helix, 20% strand | P54071 |
| B | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 417 | 47% helix, 20% strand | P54071 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 2 copies · chains A, B
- MG · Magnesium 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.75 | 0.79 | 72 | ICT, MG |
| 2 | 790 | 0.75 | 0.79 | 69 | ICT, MG |
| 3 | 367 | 0.59 | 0.76 | 33 | empty |
| 4 | 289 | 0.57 | 0.77 | 27 | empty |
| 5 | 118 | 0.47 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3541 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5H3F · Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate · the same entry in another collection · chain A against A, TM-score 1.00
- P54071 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain A 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 P54071
- Elsewhere: RCSB PDB 5H3F · PDBe 5H3F · UniProt P54071
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