MolNFT v1 · #55479 · protein
Inhibition of the pneumococcal virulence factor strh and molecular insights into N-glycan recognition and hydrolysis
2YLL · Beta-N-acetylhexosaminidase: “Inhibition of the pneumococcal virulence factor strh and molecular insights into N-glycan recognition and…”. X-ray diffraction, 2 ligands (CA, IOD), 2 pockets (best druggability 0.51). MolNFT v1 #55479…
- PDB
- 2YLL
- Type
- protein
- Length
- 436 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
- CA, IOD
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 436 | 40% helix, 17% strand | P49610 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- IOD · Iodide ion · ion · 67 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.51 | 0.80 | 23 | CA, EDO, IOD |
| 2 | 91 | 0.35 | 0.75 | 21 | IOD |
Compared structures
- 2YLL · 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 2YLL · PDBe 2YLL · UniProt P49610
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