Research workbench
Crystal structure of the hydroxyglutarate synthase in complex with 2- oxoadipate from oryza sativa
Analyse Crystal structure of the hydroxyglutarate synthase in complex with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W1K
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyglutarate synthase
- UniProt
- Q8H916
- Ligands
- OOG, NI, SO4
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyglutarate synthase | protein | 312 | 44% helix, 21% strand | Q8H916 |
| B | Hydroxyglutarate synthase | protein | 306 | 43% helix, 21% strand | Q8H916 |
| C, D | Hydroxyglutarate synthase | protein | 305 | 45% helix, 21% strand | Q8H916 |
Ligands and binding sites
- OOG · 2-oxoadipic acid · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.67 | 0.76 | 63 | empty |
| 2 | 175 | 0.65 | 0.86 | 26 | SO4 |
| 3 | 340 | 0.60 | 0.77 | 35 | empty |
| 4 | 148 | 0.58 | 0.83 | 25 | empty |
| 5 | 261 | 0.56 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1123 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 281 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6W1K · Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from… · the same entry in another collection · 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 Q8H916
- Elsewhere: RCSB PDB 6W1K · PDBe 6W1K · UniProt Q8H916
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