Research workbench
Structure of pr 10 allergen in complex with epicatechin
Analyse Structure of pr 10 allergen in complex with epicatechin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AWT
- Type
- protein
- Length
- 624 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pr 10 protein
- Ligands
- 28E, BEZ, NA
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pr 10 protein | protein | 156 | 26% helix, 46% strand | — |
Ligands and binding sites
- 28E · (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol · ligand · 6 copies · chains A, B, C, D
- BEZ · Benzoic acid · ligand · chains D
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.82 | 0.86 | 66 | 28E |
| 2 | 480 | 0.76 | 0.84 | 52 | 28E |
| 3 | 494 | 0.72 | 0.81 | 48 | 28E |
| 4 | 285 | 0.72 | 0.85 | 30 | 28E |
| 5 | 349 | 0.53 | 0.74 | 40 | empty |
Interfaces
4 interfaces between chains.
- C–D · 633 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AWT · Structure of PR 10 Allergen in complex with epicatechin · 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
- Elsewhere: RCSB PDB 6AWT · PDBe 6AWT
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.