Research workbench
Inhibition of the pneumococcal virulence factor strh and molecular insights into N-glycan recognition and hydrolysis
Analyse Inhibition of the pneumococcal virulence factor strh and molecular insights… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YL8
- Type
- protein
- Length
- 434 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- P49610
- Ligands
- MAN, NAG, MN
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 434 | 41% helix, 18% strand | P49610 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- MN · Manganese (II) ion · metal · 9 copies · chains A
- 15P · Polyethylene glycol (N=34) · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.49 | 0.79 | 19 | MAN, NAG |
Compared structures
- 2YL8 · Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan… · the same entry in another collection · chain A against A, TM-score 1.00
- P49610 · AlphaFold monomer V2.0 prediction for beta-N-acetylhexosaminidase (P49610) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P49610
- Elsewhere: RCSB PDB 2YL8 · PDBe 2YL8 · UniProt P49610
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