Research workbench
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
- 2VW1
- Type
- protein
- Length
- 658 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.39
- Source
- STREPTOCOCCUS PNEUMONIAE
- Molecule
- Sialidase B
- EC
- 3.2.1.18
- UniProt
- Q54727
- Ligands
- DAN
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.39 · 1 distinct chain · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase B (EC 3.2.1.18) | protein | 658 | 2% helix, 45% strand | Q54727 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · sugar · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.64 | 0.81 | 30 | empty |
| 2 | 186 | 0.57 | 0.81 | 28 | DAN |
| 3 | 234 | 0.53 | 0.76 | 34 | empty |
| 4 | 188 | 0.51 | 0.77 | 32 | empty |
| 5 | 62 | 0.37 | 0.79 | 16 | 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 2VW1 · PDBe 2VW1 · UniProt Q54727
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