Research workbench
Structure of pr 10 allergen ara H 8.01 in complex with 3-hydroxy-2- naphthoic acid
Analyse Structure of pr 10 allergen ara H 8.01 in complex with 3-hydroxy-2- naphthoic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AWW
- Type
- protein
- Length
- 777 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ara H 8 allergen
- UniProt
- Q6VT83
- Ligands
- BZJ, NA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ara H 8 allergen | protein | 156 | 29% helix, 46% strand | Q6VT83 |
| E | Ara H 8 allergen | protein | 153 | 27% helix, 45% strand | Q6VT83 |
Ligands and binding sites
- BZJ · 3-hydroxynaphthalene-2-carboxylic acid · ligand · 10 copies · chains B, E, D, C
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.74 | 0.83 | 45 | BZJ |
| 2 | 1005 | 0.74 | 0.77 | 99 | NA, BZJ |
| 3 | 556 | 0.73 | 0.80 | 61 | empty |
| 4 | 392 | 0.70 | 0.82 | 50 | BZJ |
| 5 | 136 | 0.70 | 0.90 | 20 | BZJ |
Interfaces
6 interfaces between chains.
- B–C · 695 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 85 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AWW · Structure of PR 10 Allergen Ara h 8.01 in complex with 3-Hydroxy-2-naphthoic acid · 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 Q6VT83
- Elsewhere: RCSB PDB 6AWW · PDBe 6AWW · UniProt Q6VT83
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