MolNFT v1 · #141109 · protein
Crystal structure of arabidopsis thaliana hppd complexed with mesotrione
5YWG · 4-hydroxyphenylpyruvate dioxygenase: “Crystal structure of arabidopsis thaliana hppd complexed with mesotrione”. X-ray diffraction, 2 ligands (92L, CO), 5 pockets (best druggability 0.71). MolNFT v1 #141109 on GenesisL1: 3D…
- PDB
- 5YWG
- Type
- protein
- Length
- 735 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- EC
- 1.13.11.27
- UniProt
- P93836
- Ligands
- 92L, CO
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 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
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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.