MolNFT v1 · #141110 · protein
Crystal structure of arabidopsis thaliana hppd complexed with Y13508
5YWH · 4-hydroxyphenylpyruvate dioxygenase: “Crystal structure of arabidopsis thaliana hppd complexed with Y13508”. X-ray diffraction, 2 ligands (92U, FE), 4 pockets (best druggability 0.75). MolNFT v1 #141110 on GenesisL1: 3D structure…
- PDB
- 5YWH
- Type
- protein
- Length
- 742 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
- 92U, FE
- Pockets
- 4 · best druggability 0.75
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, 34% strand | P93836 |
| B | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 370 | 25% helix, 34% strand | P93836 |
Ligands and binding sites
- 92U · [1,3-diethyl-2,2-bis(oxidanylidene)-2$l^{6},1,3-benzothiadiazol-5-yl]-(1-methyl-5-oxidanyl-pyrazol-4-yl)methanone · ligand · 2 copies · chains A, B
- FE · Fe (III) 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 | 440 | 0.75 | 0.84 | 48 | FE, 92U |
| 2 | 407 | 0.73 | 0.83 | 42 | 92U |
| 3 | 277 | 0.61 | 0.80 | 39 | empty |
| 4 | 263 | 0.60 | 0.79 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1671 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YWH · Crystal structure of Arabidopsis thaliana HPPD complexed with Y13508 · 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 5YWH · PDBe 5YWH · UniProt P93836
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