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Crystal structure of trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADPH, 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
- 6AJA
- Type
- protein
- Length
- 1,647 residues
- Chains
- 4
- 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
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 410 | 47% helix, 20% strand | Q387G0 |
| B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 411 | 47% helix, 20% strand | Q387G0 |
| C, D | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 413 | 47% helix, 19% strand | Q387G0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- AKG · 2-oxoglutaric acid · ligand · chains C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.78 | 0.83 | 61 | NAP, CA, AKG |
| 2 | 426 | 0.72 | 0.83 | 44 | GOL |
| 3 | 255 | 0.55 | 0.77 | 34 | empty |
| 4 | 281 | 0.55 | 0.77 | 31 | CA |
| 5 | 172 | 0.51 | 0.78 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3769 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3341 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6AJA · 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 6AJA · PDBe 6AJA · UniProt Q387G0
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