MolNFT v1 · #155999 · protein
Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with L-2-hydroxyglutarate (L-2-hg)
6LPU · D-2-hydroxyglutarate dehydrogenase, mitochondrial: “Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with L-2-hydroxyglutarate (L-2-hg)”. X-ray diffraction, 3 ligands (FAD, S2G, ZN), 13 pockets (best…
- PDB
- 6LPU
- 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, S2G, ZN
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% 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
- S2G · (2S)-2-hydroxypentanedioic acid · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.86 | 0.95 | 48 | FAD, ZN, S2G |
| 2 | 1128 | 0.85 | 0.86 | 96 | empty |
| 3 | 411 | 0.82 | 0.90 | 59 | FAD, ZN, S2G |
| 4 | 142 | 0.76 | 0.94 | 33 | empty |
| 5 | 88 | 0.74 | 0.97 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2978 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6LPU · Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with… · the same entry in another collection · chain B against B, 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 6LPU · PDBe 6LPU · UniProt Q8N465
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