MolNFT v1 · #62506 · protein
Crystal structure of pru du amandin, an allergenic protein from prunus dulcis
3EHK · Prunin: “Crystal structure of pru du amandin, an allergenic protein from prunus dulcis”. X-ray diffraction, 16 pockets (best druggability 0.83). MolNFT v1 #62506 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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