Research workbench
Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1)
Analyse Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SY1
- Type
- protein
- Length
- 1,720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
- EC
- 1.2.4.2
- UniProt
- Q96HY7
- Ligands
- TPP, MG
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial (EC 1.2.4.2) | protein | 859 | 44% helix, 14% strand | Q96HY7 |
| B | Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial (EC 1.2.4.2) | protein | 861 | 43% helix, 13% 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
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.80 | 0.82 | 95 | empty |
| 2 | 660 | 0.78 | 0.84 | 82 | TPP, MG |
| 3 | 648 | 0.78 | 0.83 | 83 | TPP, MG |
| 4 | 102 | 0.75 | 0.96 | 27 | empty |
| 5 | 526 | 0.67 | 0.78 | 67 | empty |
Interfaces
1 interface between chains.
- A–B · 5422 Ų buried · 97 hydrogen bonds · protein-protein
Compared structures
- 6SY1 · Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1) · the same entry in another collection · chain A against A, TM-score 1.00
- Q96HY7 · AlphaFold monomer V2.0 prediction for probable 2-oxoglutarate dehydrogenase E1 component… · a predicted model of the same protein · 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 Q96HY7
- Elsewhere: RCSB PDB 6SY1 · PDBe 6SY1 · UniProt Q96HY7
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