Research workbench
Pandda analysis group deposition -- crystal structure of DHTKD1 in complex with Z804566442
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
- 5RVX
- 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
- B0Y, TPP, MG
- Pockets
- 18 · 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, 13% strand | Q96HY7 |
Ligands and binding sites
- B0Y · 5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide · ligand · 2 copies · chains A, B
- 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 | 753 | 0.79 | 0.83 | 102 | TPP |
| 2 | 661 | 0.78 | 0.83 | 77 | TPP, MG |
| 3 | 644 | 0.75 | 0.81 | 51 | empty |
| 4 | 93 | 0.74 | 0.96 | 22 | empty |
| 5 | 326 | 0.72 | 0.84 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 5455 Ų buried · 98 hydrogen bonds · protein-protein
Compared structures
- 5RVX · PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z804566442 · 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 5RVX · PDBe 5RVX · UniProt Q96HY7
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