MolNFT v1 · #141113 · protein
Crystal structure of arabidopsis thaliana hppd complexed with benquitrione-methyl
5YWK · 4-hydroxyphenylpyruvate dioxygenase: “Crystal structure of arabidopsis thaliana hppd complexed with benquitrione-methyl”. X-ray diffraction, 2 ligands (92X, CO), 4 pockets (best druggability 0.69). MolNFT v1 #141113 on GenesisL1: 3D…
- PDB
- 5YWK
- 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
- 92X, CO
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 372 | 26% helix, 33% strand | P93836 |
| B | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 368 | 26% helix, 35% strand | P93836 |
Ligands and binding sites
- 92X · 1,5-dimethyl-3-(2-methylphenyl)-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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.69 | 0.80 | 46 | 92X |
| 2 | 449 | 0.68 | 0.80 | 49 | 92X |
| 3 | 305 | 0.62 | 0.79 | 36 | empty |
| 4 | 258 | 0.62 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1630 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YWK · Crystal structure of Arabidopsis thaliana HPPD complexed with Benquitrione-Methyl · 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 5YWK · PDBe 5YWK · UniProt P93836
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