Research workbench
Crystal structure of phl P 4, a grass pollen allergen with glucose dehydrogenase activity
Analyse Crystal structure of phl P 4, a grass pollen allergen with glucose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TSJ
- Type
- protein
- Length
- 978 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pollen allergen phl P 4
- UniProt
- Q5ZQK4
- Ligands
- FDA, NA, SO4
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pollen allergen phl P 4 | protein | 489 | 36% helix, 22% strand | Q5ZQK4 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.87 | 0.89 | 104 | FDA |
| 2 | 953 | 0.86 | 0.88 | 114 | FDA |
| 3 | 108 | 0.36 | 0.74 | 25 | empty |
| 4 | 63 | 0.32 | 0.76 | 12 | empty |
| 5 | 61 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 3TSJ · Crystal structure of Phl p 4, a grass pollen allergen with glucose dehydrogenase activity · 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 Q5ZQK4
- Elsewhere: RCSB PDB 3TSJ · PDBe 3TSJ · UniProt Q5ZQK4
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