Research workbench
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-mal)
Analyse Crystal structure of human D-2-hydroxyglutarate dehydrogenase 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
- 6LPQ
- Type
- protein
- Length
- 933 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-2-hydroxyglutarate dehydrogenase, mitochondrial
- EC
- 1.1.99.-
- UniProt
- Q8N465
- Ligands
- FAD, MLT, ZN
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-2-hydroxyglutarate dehydrogenase, mitochondrial (EC 1.1.99.-) | protein | 466 | 36% helix, 22% strand | Q8N465 |
| B | D-2-hydroxyglutarate dehydrogenase, mitochondrial (EC 1.1.99.-) | protein | 467 | 37% helix, 22% strand | Q8N465 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MLT · D-malate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.86 | 0.87 | 91 | empty |
| 2 | 375 | 0.85 | 0.94 | 55 | FAD, MLT |
| 3 | 420 | 0.84 | 0.92 | 53 | FAD, MLT |
| 4 | 196 | 0.78 | 0.93 | 41 | empty |
| 5 | 151 | 0.72 | 0.91 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2933 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6LPQ · Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N465 · AlphaFold monomer V2.0 prediction for D-2-hydroxyglutarate dehydrogenase, mitochondrial… · 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 Q8N465
- Elsewhere: RCSB PDB 6LPQ · PDBe 6LPQ · UniProt Q8N465
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