Research workbench
Pandda analysis group deposition -- crystal structure of DHTKD1 in complex with Z437516460
Analyse Pandda analysis group deposition -- crystal structure of DHTKD1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5RVY
- Type
- protein
- Length
- 1,734 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, NWY, MG
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 867 | 43% helix, 14% strand | Q96HY7 |
| B | Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial (EC 1.2.4.2) | protein | 867 | 43% helix, 14% strand | Q96HY7 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- NWY · N-[(6-methylpyridin-3-yl)methyl]cyclobutanecarboxamide · ligand · 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.79 | 0.84 | 77 | TPP |
| 2 | 659 | 0.78 | 0.83 | 79 | TPP, MG |
| 3 | 690 | 0.77 | 0.82 | 60 | NWY |
| 4 | 732 | 0.74 | 0.80 | 104 | empty |
| 5 | 96 | 0.74 | 0.96 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 5461 Ų buried · 95 hydrogen bonds · protein-protein
Compared structures
- 5RVY · PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z437516460 · 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 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 5RVY · PDBe 5RVY · UniProt Q96HY7
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