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
- 2YL9
- Type
- protein
- Length
- 1,641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- P49610
- Ligands
- NAG, BMA, MAN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 411 | 42% helix, 18% strand | P49610 |
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 409 | 40% helix, 18% strand | P49610 |
| C | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 410 | 40% helix, 18% strand | P49610 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.82 | 0.83 | 114 | NAG, EDO |
| 2 | 1164 | 0.81 | 0.83 | 106 | MAN, NAG, EDO |
| 3 | 992 | 0.70 | 0.75 | 75 | empty |
| 4 | 138 | 0.49 | 0.79 | 23 | MAN, NAG |
| 5 | 133 | 0.44 | 0.76 | 23 | MAN, NAG |
Interfaces
3 interfaces between chains.
- A–D · 998 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 957 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 214 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YL9 · 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 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 P49610
- Elsewhere: RCSB PDB 2YL9 · PDBe 2YL9 · UniProt P49610
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