MolNFT v1 · #149551 · protein
Structure of pseudomonas aeruginosa isocitrate dehydrogenase, idh
6G3U: “Structure of pseudomonas aeruginosa isocitrate dehydrogenase, idh”. X-ray diffraction, 2 ligands (NAP, AKG), 19 pockets (best druggability 0.82). MolNFT v1 #149551 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6G3U
- Type
- protein
- Length
- 1,467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- UniProt
- Q9I0L4
- Ligands
- NAP, AKG
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase | protein | 737 | 48% helix, 16% strand | Q9I0L4 |
| B | Isocitrate dehydrogenase | protein | 730 | 44% helix, 16% strand | Q9I0L4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
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 | 810 | 0.82 | 0.85 | 92 | empty |
| 2 | 156 | 0.81 | 0.97 | 31 | empty |
| 3 | 1045 | 0.81 | 0.82 | 78 | NAP, AKG |
| 4 | 105 | 0.78 | 0.98 | 27 | empty |
| 5 | 365 | 0.77 | 0.87 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6G3U · Structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, IDH · 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 Q9I0L4
- Elsewhere: RCSB PDB 6G3U · PDBe 6G3U · UniProt Q9I0L4
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