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Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-HG)
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
- 6LPP
- Type
- protein
- Length
- 933 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Homo sapiens
- Molecule
- D-2-hydroxyglutarate dehydrogenase, mitochondrial
- EC
- 1.1.99.-
- UniProt
- Q8N465
- Ligands
- FAD, 2HG, ZN
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.65 · 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 | 37% helix, 22% strand | Q8N465 |
| B | D-2-hydroxyglutarate dehydrogenase, mitochondrial (EC 1.1.99.-) | protein | 467 | 38% helix, 22% strand | Q8N465 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 2HG · (2R)-2-hydroxypentanedioic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.85 | 0.86 | 91 | empty |
| 2 | 450 | 0.84 | 0.92 | 64 | FAD, ZN, 2HG |
| 3 | 405 | 0.84 | 0.92 | 52 | FAD, ZN, 2HG |
| 4 | 176 | 0.77 | 0.94 | 37 | empty |
| 5 | 113 | 0.76 | 0.96 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2930 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 6LPP · Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with… · 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 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 Q8N465
- Elsewhere: RCSB PDB 6LPP · PDBe 6LPP · UniProt Q8N465
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