Research workbench
Ternary complex of isocitrate dehydrogenase from the hyperthermophile aeropyrum pernix
Analyse Ternary complex of isocitrate dehydrogenase from the hyperthermophile aeropyrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XKD
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- Q9YE81
- Ligands
- NAP, ICT, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 427 | 46% helix, 18% strand | Q9YE81 |
| B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 419 | 43% helix, 18% strand | Q9YE81 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ICT · Isocitric acid · ligand · 2 copies · chains A, 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.78 | 0.83 | 67 | CA, NAP, ICT |
| 2 | 729 | 0.68 | 0.76 | 77 | CA, NAP, ICT |
| 3 | 75 | 0.64 | 0.91 | 21 | empty |
| 4 | 107 | 0.53 | 0.82 | 16 | empty |
| 5 | 93 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3279 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1XKD · Ternary complex of Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix · 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 Q9YE81
- Elsewhere: RCSB PDB 1XKD · PDBe 1XKD · UniProt Q9YE81
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.