Research workbench
4-hydroxyphenylpyruvate dioxygenase
Analyse 4-hydroxyphenylpyruvate dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SP8
- Type
- protein
- Length
- 1,559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- Ligands
- FE2
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase | protein | 388 | 28% helix, 33% strand | — |
| B | 4-hydroxyphenylpyruvate dioxygenase | protein | 392 | 29% helix, 34% strand | — |
| C | 4-hydroxyphenylpyruvate dioxygenase | protein | 386 | 29% helix, 33% strand | — |
| D | 4-hydroxyphenylpyruvate dioxygenase | protein | 393 | 29% helix, 33% strand | — |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.86 | 0.88 | 85 | empty |
| 2 | 967 | 0.85 | 0.86 | 99 | empty |
| 3 | 1091 | 0.83 | 0.84 | 90 | FE2 |
| 4 | 1083 | 0.83 | 0.84 | 94 | empty |
| 5 | 99 | 0.69 | 0.93 | 33 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1673 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1632 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 116 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1SP8 · 4-Hydroxyphenylpyruvate Dioxygenase · 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
- Elsewhere: RCSB PDB 1SP8 · PDBe 1SP8
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