Research workbench
Crystal structure of the acidaminococcus fermentans (R)-2- hydroxyglutaryl-CoA dehydratase component a
Analyse Crystal structure of the acidaminococcus fermentans (R)-2- hydroxyglutaryl-CoA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HUX
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activator of (R)-2-hydroxyglutaryl-CoA dehydratase
- UniProt
- P11568
- Ligands
- ADP, SF4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Activator of (R)-2-hydroxyglutaryl-CoA dehydratase | protein | 259 | 43% helix, 23% strand | P11568 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.63 | 0.80 | 46 | ADP |
| 2 | 295 | 0.62 | 0.80 | 47 | ADP |
| 3 | 108 | 0.40 | 0.75 | 20 | SF4 |
| 4 | 60 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1HUX · Crystal structure of the acidaminococcus fermentans (R)-2-hydroxyglutaryl-CoA dehydratase… · the same entry in another collection · chain A against A, TM-score 1.00
- P11568 · AlphaFold monomer V2.0 prediction for (R)-2-hydroxyglutaryl-CoA dehydratase activating… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P11568
- Elsewhere: RCSB PDB 1HUX · PDBe 1HUX · UniProt P11568
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