Research workbench
Aad-1 bound to the vanadyl ion and succinate
Analyse Aad-1 bound to the vanadyl ion and succinate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BK9
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase
- EC
- 1.14.11.44
- UniProt
- P83310
- Ligands
- VVO, PO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 289 | 25% helix, 28% strand | P83310 |
| B | (R)-PHENOXYPROPIONATE/ALPHA-ketoglutarate-dioxygenase (EC 1.14.11.44) | protein | 267 | 20% helix, 29% strand | P83310 |
Ligands and binding sites
- VVO · oxovanadium(2+) · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.79 | 0.92 | 46 | SIN, VVO |
| 2 | 274 | 0.67 | 0.83 | 36 | VVO |
| 3 | 373 | 0.62 | 0.78 | 39 | PO4 |
| 4 | 320 | 0.60 | 0.78 | 31 | empty |
| 5 | 117 | 0.49 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1024 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 P83310
- Elsewhere: RCSB PDB 5BK9 · PDBe 5BK9 · UniProt P83310
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