MolNFT v1 · #54715 · protein
Crystal structure of drosophila grass clip serine protease of toll pathway
2XXL · Gram-positive specific serine protease, isoform B: “Crystal structure of drosophila grass clip serine protease of toll pathway”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 10 pockets (best druggability 0.46). MolNFT v1 #54715 on…
- PDB
- 2XXL
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gram-positive specific serine protease, isoform B
- EC
- 3.4.21.4
- UniProt
- Q9VB68
- Ligands
- NAG, BMA, FUC, CA
- Pockets
- 10 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gram-positive specific serine protease, isoform B (EC 3.4.21.4) | protein | 354 | 20% helix, 35% strand | Q9VB68 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.46 | 0.77 | 18 | empty |
| 2 | 78 | 0.44 | 0.81 | 21 | empty |
| 3 | 147 | 0.42 | 0.75 | 25 | empty |
| 4 | 61 | 0.42 | 0.81 | 14 | empty |
| 5 | 108 | 0.40 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 64 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2XXL · Crystal structure of drosophila Grass clip serine protease of Toll pathway · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VB68 · AlphaFold monomer V2.0 prediction for serine protease grass (Q9VB68) · 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 Q9VB68
- Elsewhere: RCSB PDB 2XXL · PDBe 2XXL · UniProt Q9VB68
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