Research workbench
Crystal structure of fatty acid alpha-dioxygenase (arabidopsis thaliana)
Analyse Crystal structure of fatty acid alpha-dioxygenase (arabidopsis thaliana) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HHR
- Type
- protein
- Length
- 640 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-dioxygenase
- UniProt
- Q9SGH6
- Ligands
- HEM, BNG, CA, CL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-dioxygenase | protein | 640 | 47% helix, 9% strand | Q9SGH6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- BNG · nonyl beta-D-glucopyranoside · ligand · chains A
- CA · Calcium ion · metal · 8 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A
- IMD · Imidazole · additive · chains A
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.84 | 0.90 | 52 | HEM, IMD |
| 2 | 89 | 0.71 | 0.94 | 28 | CL |
| 3 | 188 | 0.51 | 0.78 | 22 | P6G |
| 4 | 244 | 0.49 | 0.74 | 29 | PGE |
| 5 | 110 | 0.47 | 0.80 | 25 | empty |
Compared structures
- 4HHR · Crystal Structure of fatty acid alpha-dioxygenase (Arabidopsis thaliana) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SGH6 · AlphaFold monomer V2.0 prediction for alpha-dioxygenase 1 (Q9SGH6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9SGH6
- Elsewhere: RCSB PDB 4HHR · PDBe 4HHR · UniProt Q9SGH6
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