Research workbench
Crystal structure of pru du amandin, an allergenic protein from prunus dulcis
Analyse Crystal structure of pru du amandin, an allergenic protein from prunus dulcis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EHK
- Type
- protein
- Length
- 2,304 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prunin
- UniProt
- Q43607
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Prunin | protein | 384 | 14% helix, 37% strand | Q43607 |
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.83 | 0.86 | 66 | empty |
| 2 | 727 | 0.83 | 0.86 | 65 | empty |
| 3 | 498 | 0.77 | 0.84 | 49 | empty |
| 4 | 347 | 0.76 | 0.86 | 34 | empty |
| 5 | 695 | 0.73 | 0.80 | 68 | empty |
Interfaces
15 interfaces between chains.
- A–C · 2799 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 2795 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 2794 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2780 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2769 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3EHK · Crystal structure of Pru du amandin, an allergenic protein from prunus dulcis · the same entry in another collection · chain C against C, TM-score 1.00
- Q43607 · AlphaFold monomer V2.0 prediction for prunin 1 pru du 6 (Q43607) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q43607
- Elsewhere: RCSB PDB 3EHK · PDBe 3EHK · UniProt Q43607
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