MolNFT v1 · #117224 · protein
Crystal structure of pecan (carya illinoinensis) vicilin, a new food allergen
5E1R · 7S vicilin: “Crystal structure of pecan (carya illinoinensis) vicilin, a new food allergen”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.75). MolNFT v1 #117224 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5E1R
- Type
- protein
- Length
- 2,143 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7S vicilin
- UniProt
- B3STU4
- Ligands
- CU
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7S vicilin | protein | 357 | 17% helix, 42% strand | B3STU4 |
| B | 7S vicilin | protein | 355 | 16% helix, 42% strand | B3STU4 |
| C | 7S vicilin | protein | 358 | 16% helix, 42% strand | B3STU4 |
| D | 7S vicilin | protein | 357 | 16% helix, 42% strand | B3STU4 |
| E | 7S vicilin | protein | 358 | 16% helix, 42% strand | B3STU4 |
| F | 7S vicilin | protein | 358 | 16% helix, 41% strand | B3STU4 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.75 | 0.99 | 17 | MPD |
| 2 | 65 | 0.75 | 0.99 | 19 | MPD |
| 3 | 63 | 0.75 | 0.99 | 19 | MPD |
| 4 | 59 | 0.75 | 1.00 | 18 | MPD |
| 5 | 61 | 0.74 | 0.99 | 17 | MPD |
Interfaces
8 interfaces between chains.
- D–E · 2708 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 2686 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2656 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2621 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2522 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5E1R · Crystal structure of pecan (carya illinoinensis) vicilin, a new food allergen · the same entry in another collection · chain F against F, TM-score 1.00
- B3STU4 · AlphaFold monomer V2.0 prediction for vicilin car I 2.0101 (B3STU4) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 B3STU4
- Elsewhere: RCSB PDB 5E1R · PDBe 5E1R · UniProt B3STU4
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