MolNFT v1 · #51107 · protein
Complex with isocitrate and the protein isocitrate dehydrogenase from the psychrophilic bacterium desulfotalea psychrophila
2UXR: “Complex with isocitrate and the protein isocitrate dehydrogenase from the psychrophilic bacterium…”. X-ray diffraction, 2 ligands (ICT, MG), 8 pockets (best druggability 0.83). MolNFT v1 #51107 on GenesisL1: 3D structure, binding…
- PDB
- 2UXR
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- UniProt
- Q6AQ66
- Ligands
- ICT, MG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase | protein | 402 | 45% helix, 22% strand | Q6AQ66 |
| B | Isocitrate dehydrogenase | protein | 395 | 39% helix, 24% strand | Q6AQ66 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · 3 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.83 | 0.99 | 22 | empty |
| 2 | 854 | 0.77 | 0.81 | 56 | ICT |
| 3 | 773 | 0.77 | 0.81 | 56 | ICT, MG |
| 4 | 57 | 0.65 | 0.94 | 18 | empty |
| 5 | 269 | 0.53 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 4346 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 2UXR · Complex with isocitrate and the protein isocitrate dehydrogenase from the psychrophilic… · 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 Q6AQ66
- Elsewhere: RCSB PDB 2UXR · PDBe 2UXR · UniProt Q6AQ66
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