Research workbench
Crystal structure of mite allergen der F 1
Analyse Crystal structure of mite allergen der F 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VPK
- Type
- protein
- Length
- 669 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Der F 1 variant
- UniProt
- I2CMD3
- Ligands
- NAG, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Der F 1 variant | protein | 223 | 28% helix, 24% strand | I2CMD3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.83 | 0.85 | 89 | SO4 |
| 2 | 70 | 0.41 | 0.80 | 16 | empty |
| 3 | 98 | 0.34 | 0.73 | 20 | empty |
| 4 | 59 | 0.33 | 0.76 | 13 | SO4 |
| 5 | 86 | 0.31 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 756 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VPK · Crystal structure of mite allergen der F 1 · 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 I2CMD3
- Elsewhere: RCSB PDB 5VPK · PDBe 5VPK · UniProt I2CMD3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.