MolNFT v1 · #141161 · protein
Crystal structure of arabidopsis thaliana hppd complexed with benquitrione
5YY7 · 4-hydroxyphenylpyruvate dioxygenase: “Crystal structure of arabidopsis thaliana hppd complexed with benquitrione”. X-ray diffraction, 2 ligands (94L, CO), 8 pockets (best druggability 0.71). MolNFT v1 #141161 on GenesisL1: 3D…
- PDB
- 5YY7
- Type
- protein
- Length
- 740 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
- 94L, CO
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 367 | 23% helix, 32% strand | P93836 |
| B | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 373 | 22% helix, 30% strand | P93836 |
Ligands and binding sites
- 94L · 3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2, 4-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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.71 | 0.90 | 37 | empty |
| 2 | 507 | 0.70 | 0.79 | 45 | CO, 94L |
| 3 | 419 | 0.68 | 0.80 | 45 | 94L |
| 4 | 247 | 0.65 | 0.83 | 36 | empty |
| 5 | 270 | 0.61 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1623 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YY7 · Crystal structure of Arabidopsis thaliana HPPD complexed with Benquitrione · 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 5YY7 · PDBe 5YY7 · UniProt P93836
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