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Crystal structure of the NanB sialidase from Streptococcus pneumoniae
Analyse Crystal structure of the NanB sialidase from Streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VW0
- Type
- protein
- Length
- 657 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- STREPTOCOCCUS PNEUMONIAE
- Molecule
- Sialidase B
- EC
- 3.2.1.18
- UniProt
- Q54727
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase B (EC 3.2.1.18) | protein | 657 | 3% helix, 45% strand | Q54727 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.63 | 0.80 | 35 | empty |
| 2 | 274 | 0.62 | 0.80 | 23 | GOL |
| 3 | 250 | 0.54 | 0.76 | 33 | empty |
| 4 | 196 | 0.49 | 0.76 | 26 | empty |
| 5 | 69 | 0.37 | 0.77 | 15 | empty |
Compared structures
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 Q54727
- Elsewhere: RCSB PDB 2VW0 · PDBe 2VW0 · UniProt Q54727
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