MolNFT v1 · #142901 · protein
Crystal structure of trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and CA2+
6AJB · Isocitrate dehydrogenase [NADP]: “Crystal structure of trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH…”. X-ray diffraction, 3 ligands (NAD, AKG, CA), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6AJB
- Type
- protein
- Length
- 1,641 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
- NAD, AKG, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 410 | 47% helix, 19% strand | Q387G0 |
| B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 411 | 46% helix, 19% strand | Q387G0 |
| C | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 407 | 47% helix, 20% strand | Q387G0 |
| D | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 413 | 44% helix, 19% strand | Q387G0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.78 | 0.82 | 72 | NAD, AKG, CA |
| 2 | 602 | 0.75 | 0.82 | 64 | empty |
| 3 | 559 | 0.63 | 0.75 | 58 | NAD |
| 4 | 286 | 0.56 | 0.77 | 39 | CA |
| 5 | 242 | 0.50 | 0.75 | 38 | CA |
Interfaces
3 interfaces between chains.
- C–D · 3784 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 3331 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 756 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6AJB · 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 6AJB · PDBe 6AJB · UniProt Q387G0
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