MolNFT v1 · #139464 · protein
Crystal structure of arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (athppd) complexed with its substrate 4- hydroxyphenylpyruvate acid (hppa)
5XGK: “Crystal structure of arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (athppd) complexed with its…”. X-ray diffraction, 2 ligands (TYF, FE), 15 pockets (best druggability 0.77). MolNFT v1 #139464 on GenesisL1: 3D structure…
- PDB
- 5XGK
- Type
- protein
- Length
- 1,478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- EC
- 1.13.11.27
- UniProt
- P93836
- Ligands
- TYF, FE
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 368 | 26% helix, 34% strand | P93836 |
| B | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 367 | 26% helix, 32% strand | P93836 |
| C | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 374 | 26% helix, 32% strand | P93836 |
| D | 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) | protein | 369 | 26% helix, 34% strand | P93836 |
Ligands and binding sites
- TYF · (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid · ligand · chains A
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.77 | 0.79 | 104 | ACT |
| 2 | 58 | 0.70 | 0.97 | 28 | empty |
| 3 | 462 | 0.66 | 0.78 | 42 | TYF, FE |
| 4 | 632 | 0.65 | 0.75 | 67 | empty |
| 5 | 451 | 0.64 | 0.77 | 43 | FE |
Interfaces
4 interfaces between chains.
- C–D · 1610 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1581 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5XGK · Crystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (AtHPPD)… · 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 5XGK · PDBe 5XGK · UniProt P93836
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