Research workbench
Crystal structure of the complex of antibody and the allergen bla G 2
Analyse Crystal structure of the complex of antibody and the allergen bla G 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NR6
- Type
- protein
- Length
- 1,508 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartic protease bla G 2; Antibody light chain; Antibody heavy chain
- EC
- 3.4.23.-
- UniProt
- P54958
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aspartic protease bla G 2 (EC 3.4.23.-) | protein | 330 | 12% helix, 48% strand | P54958 |
| C, E | Antibody light chain | protein | 211 | 5% helix, 50% strand | — |
| D, F | Antibody heavy chain | protein | 213 | 4% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.70 | 0.78 | 51 | empty |
| 2 | 658 | 0.69 | 0.77 | 46 | empty |
| 3 | 690 | 0.67 | 0.76 | 87 | empty |
| 4 | 408 | 0.65 | 0.79 | 40 | empty |
| 5 | 454 | 0.59 | 0.74 | 51 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1716 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1611 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 519 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 505 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan, 2 modified (disulfide, N-glycosylation, oxidation).
Compared structures
- 2NR6 · Crystal structure of the complex of antibody and the allergen Bla g 2 · the same entry in another collection · chain F against F, TM-score 1.00
- P54958 · AlphaFold monomer V2.0 prediction for aspartic protease bla G 2 (P54958) · a predicted model of the same protein · 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 P54958
- Elsewhere: RCSB PDB 2NR6 · PDBe 2NR6 · UniProt P54958
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