Research workbench
Crystal structure of the strawberry pathogenesis-related 10 (pr-10) fra a 1E protein (form B)
Analyse Crystal structure of the strawberry pathogenesis-related 10 (pr-10) fra a 1E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C9I
- Type
- protein
- Length
- 968 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major strawberry allergen fra a 1-E
- UniProt
- Q256S2
- Ligands
- KXN
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Major strawberry allergen fra a 1-E | protein | 162 | 25% helix, 43% strand | Q256S2 |
| E | Major strawberry allergen fra a 1-E | protein | 158 | 26% helix, 39% strand | Q256S2 |
Ligands and binding sites
- KXN · (2R,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol · ligand · chains F
- GOL · Glycerol · additive · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.84 | 0.86 | 65 | GOL |
| 2 | 490 | 0.82 | 0.88 | 60 | empty |
| 3 | 774 | 0.81 | 0.83 | 61 | empty |
| 4 | 792 | 0.79 | 0.82 | 56 | empty |
| 5 | 678 | 0.78 | 0.83 | 59 | GOL |
Interfaces
5 interfaces between chains.
- A–C · 667 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 442 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 421 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 248 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4C9I · Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 1E protein… · the same entry in another collection · chain F against F, TM-score 1.00
- Q256S2 · AlphaFold monomer V2.0 prediction for major strawberry allergen fra a 1-E (Q256S2) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q256S2
- Elsewhere: RCSB PDB 4C9I · PDBe 4C9I · UniProt Q256S2
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