MolNFT v1 · #51106 · protein
Isocitrate dehydrogenase from the psychrophilic bacterium desulfotalea psychrophila: biochemical properties and crystal structure analysis
2UXQ · Isocitrate dehydrogenase native: “Isocitrate dehydrogenase from the psychrophilic bacterium desulfotalea psychrophila: biochemical properties…”. X-ray diffraction, 2 ligands (MG, SO4), 19 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 2UXQ
- Type
- protein
- Length
- 1,607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase native
- UniProt
- Q6AQ66
- Ligands
- MG, SO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Isocitrate dehydrogenase native | protein | 402 | 45% helix, 22% strand | Q6AQ66 |
| B | Isocitrate dehydrogenase native | protein | 401 | 46% helix, 22% strand | Q6AQ66 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.84 | 0.99 | 27 | empty |
| 2 | 169 | 0.83 | 0.98 | 25 | empty |
| 3 | 807 | 0.76 | 0.80 | 58 | GOL, SO4, MG |
| 4 | 820 | 0.75 | 0.79 | 58 | GOL, SO4 |
| 5 | 846 | 0.74 | 0.79 | 67 | GOL, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 3926 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3892 Ų buried · 67 hydrogen bonds · protein-protein
- B–D · 480 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2UXQ · Isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila… · 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 2UXQ · PDBe 2UXQ · UniProt Q6AQ66
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