MolNFT v1 · #155994 · protein
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-hg)
6LPP · D-2-hydroxyglutarate dehydrogenase, mitochondrial: “Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-hg)”. X-ray diffraction, 3 ligands (FAD, 2HG, ZN), 13 pockets (best…
- PDB
- 6LPP
- 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, 2HG, ZN
- Pockets
- 13 · best druggability 0.85
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 | 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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