Research workbench
Crystal structure of arabidopsis thaliana hppd truncated mutant complexed with benquitrione
Analyse Crystal structure of arabidopsis thaliana hppd truncated mutant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YY6
- Type
- protein
- Length
- 371 residues
- Chains
- 1
- 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
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 371 | 28% helix, 34% 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 · chains A
- CO · Cobalt (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.68 | 0.79 | 45 | CO, 94L |
| 2 | 64 | 0.36 | 0.78 | 14 | empty |
| 3 | 69 | 0.36 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5YY6 · Crystal structure of Arabidopsis thaliana HPPD truncated mutant complexed with… · 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 5YY6 · PDBe 5YY6 · UniProt P93836
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