Research workbench
Crystal structure of bermuda grass isoallergen BG60 provides insight into the various cross-allergenicity of the pollen group 4 allergens
Analyse Crystal structure of bermuda grass isoallergen BG60 provides insight into the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DNS
- Type
- protein
- Length
- 971 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-linked oxidoreductase BG60
- UniProt
- Q5QJ60
- Ligands
- FAD, NAG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-linked oxidoreductase BG60 | protein | 486 | 36% helix, 22% strand | Q5QJ60 |
| B | FAD-linked oxidoreductase BG60 | protein | 485 | 34% helix, 22% strand | Q5QJ60 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.83 | 0.89 | 67 | FAD |
| 2 | 1089 | 0.82 | 0.84 | 73 | empty |
| 3 | 475 | 0.81 | 0.88 | 61 | FAD |
| 4 | 53 | 0.72 | 0.99 | 15 | empty |
| 5 | 204 | 0.58 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1050 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 glycan (flavinylation, N-glycosylation).
Compared structures
- 4DNS · Crystal structure of Bermuda grass isoallergen BG60 provides insight into the various… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5QJ60 · AlphaFold monomer V2.0 prediction for berberine bridge enzyme-like cyn D 4 (Q5QJ60) · a predicted model of the same protein · chain B 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 Q5QJ60
- Elsewhere: RCSB PDB 4DNS · PDBe 4DNS · UniProt Q5QJ60
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