Research workbench
Crystal structure of Arabidopsis thaliana HPPD complexed with Mesotrione
Analyse Crystal structure of Arabidopsis thaliana HPPD complexed with Mesotrione in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YWG
- Type
- protein
- Length
- 735 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.603
- Source
- Arabidopsis thaliana
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- EC
- 1.13.11.27
- UniProt
- P93836
- Ligands
- 92L, CO
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.603 · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 366 | 25% helix, 34% strand | P93836 |
| B | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 369 | 25% helix, 33% strand | P93836 |
Ligands and binding sites
- 92L · 2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.71 | 0.82 | 41 | 92L |
| 2 | 404 | 0.70 | 0.81 | 51 | 92L |
| 3 | 335 | 0.62 | 0.79 | 35 | empty |
| 4 | 286 | 0.61 | 0.79 | 36 | empty |
| 5 | 51 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1627 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YWG · Crystal structure of arabidopsis thaliana hppd complexed with mesotrione · the same entry in another collection · chain A against A, TM-score 1.00
- P93836 · AlphaFold monomer V2.0 prediction for 4-hydroxyphenylpyruvate dioxygenase (P93836) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P93836
- Elsewhere: RCSB PDB 5YWG · PDBe 5YWG · UniProt P93836
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