Research workbench
Crystal structure of a major house dust mite allergen, derf 2
Analyse Crystal structure of a major house dust mite allergen, derf 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F08
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mite allergen der F II
- UniProt
- Q00855
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mite allergen der F II | protein | 129 | 2% helix, 57% strand | Q00855 |
Ligands and binding sites
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.76 | 0.80 | 79 | empty |
| 2 | 424 | 0.70 | 0.81 | 49 | empty |
| 3 | 53 | 0.69 | 0.97 | 26 | empty |
| 4 | 58 | 0.68 | 0.96 | 30 | empty |
| 5 | 117 | 0.43 | 0.77 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 629 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 609 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 581 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 413 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2F08 · Crystal structure of a major house dust mite allergen, Derf 2 · the same entry in another collection · chain D against D, 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 0.95
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 2F08 · PDBe 2F08 · UniProt Q00855
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