Research workbench
Crystal structure of ara H 8.0201
Analyse Crystal structure of ara H 8.0201 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V8S
- Type
- protein
- Length
- 2,430 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ara H 8 allergen isoform
- UniProt
- B0YIU5
- Ligands
- 2AN, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, L, M, N, O, P | Ara H 8 allergen isoform | protein | 152 | 30% helix, 47% strand | B0YIU5 |
| J | Ara H 8 allergen isoform | protein | 151 | 30% helix, 47% strand | B0YIU5 |
| K | Ara H 8 allergen isoform | protein | 151 | 30% helix, 46% strand | B0YIU5 |
Ligands and binding sites
- 2AN · 8-anilino-1-naphthalene sulfonate · ligand · 102 copies · chains A, F, G, E, B, C, D, H, I, O, N, J, K, L, M, P
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.85 | 0.90 | 62 | 2AN |
| 2 | 591 | 0.85 | 0.90 | 58 | 2AN |
| 3 | 560 | 0.85 | 0.90 | 60 | 2AN |
| 4 | 580 | 0.85 | 0.90 | 63 | 2AN |
| 5 | 635 | 0.84 | 0.89 | 68 | 2AN, SO4 |
Interfaces
31 interfaces between chains.
- F–H · 881 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 879 Ų buried · 11 hydrogen bonds · protein-protein
- I–O · 855 Ų buried · 8 hydrogen bonds · protein-protein
- N–P · 855 Ų buried · 7 hydrogen bonds · protein-protein
- N–O · 347 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6V8S · Crystal structure of Ara h 8.0201 · 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
- Every structure of UniProt B0YIU5
- Elsewhere: RCSB PDB 6V8S · PDBe 6V8S · UniProt B0YIU5
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