MolNFT v1 · #165693 · protein
Structure of the 2-oxoadipate dehydrogenase DHTKD1
6U3J · 2-oxoglutarate dehydrogenase E1 component DHKTD1…: “Structure of the 2-oxoadipate dehydrogenase DHTKD1”. X-ray diffraction, 2 ligands (TPP, MG), 20 pockets (best druggability 0.79). MolNFT v1 #165693 on GenesisL1: 3D structure…
- PDB
- 6U3J
- Type
- protein
- Length
- 1,752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
- EC
- 1.2.4.2
- UniProt
- Q96HY7
- Ligands
- TPP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial (EC 1.2.4.2) | protein | 876 | 41% helix, 14% strand | Q96HY7 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.79 | 0.84 | 85 | TPP |
| 2 | 728 | 0.79 | 0.83 | 83 | TPP |
| 3 | 686 | 0.77 | 0.82 | 91 | empty |
| 4 | 773 | 0.75 | 0.79 | 54 | empty |
| 5 | 298 | 0.72 | 0.85 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 5449 Ų buried · 85 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- Q96HY7 · AlphaFold monomer V2.0 prediction for probable 2-oxoglutarate dehydrogenase E1 component… · a predicted model of the same protein · chain B 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 Q96HY7
- Elsewhere: RCSB PDB 6U3J · PDBe 6U3J · UniProt Q96HY7
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