Research workbench
Crystal structure of trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+, alpha-ketoglutarate and CA2+
Analyse Crystal structure of trypanosoma brucei glycosomal isocitrate dehydrogenase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AJ8
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- Q387G0
- Ligands
- NAP, AKG, CA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 413 | 47% helix, 20% strand | Q387G0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- AKG · 2-oxoglutaric acid · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.74 | 0.98 | 26 | empty |
| 2 | 259 | 0.52 | 0.76 | 40 | CA, AKG |
| 3 | 213 | 0.51 | 0.77 | 35 | empty |
| 4 | 183 | 0.48 | 0.76 | 21 | empty |
| 5 | 187 | 0.48 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3353 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6AJ8 · Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex… · 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 Q387G0
- Elsewhere: RCSB PDB 6AJ8 · PDBe 6AJ8 · UniProt Q387G0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.