Research workbench
Structure of the house dust mite allergen der F 2: implications for function and molecular basis of IgE cross- reactivity
Analyse Structure of the house dust mite allergen der F 2: implications for function… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XWV
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Der F II
- UniProt
- Q00855
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Der F II | protein | 129 | 2% helix, 53% strand | Q00855 |
Ligands and binding sites
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.86 | 0.94 | 53 | XPE |
| 2 | 426 | 0.86 | 0.92 | 52 | PE3 |
| 3 | 217 | 0.51 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 223 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1XWV · Structure of the house dust mite allergen Der f 2: Implications for function and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00855 · AlphaFold monomer V2.0 prediction for mite group 2 allergen der F 2 (Q00855) · 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 Q00855
- Elsewhere: RCSB PDB 1XWV · PDBe 1XWV · UniProt Q00855
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