Research workbench
Crystal structure of B/PERTH neuraminidase
Analyse Crystal structure of B/PERTH neuraminidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K36
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q3S340
- Ligands
- MAN, NAG, BMA, CA, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase (EC 3.2.1.18) | protein | 389 | 1% helix, 47% strand | Q3S340 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
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 | 1033 | 0.82 | 0.83 | 102 | SO4, GOL |
| 2 | 149 | 0.81 | 0.97 | 30 | empty |
| 3 | 136 | 0.78 | 0.96 | 28 | empty |
| 4 | 161 | 0.45 | 0.76 | 29 | empty |
| 5 | 143 | 0.44 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3K36 · Crystal Structure of B/Perth Neuraminidase · the same entry in another collection · chain A 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 Q3S340
- Elsewhere: RCSB PDB 3K36 · PDBe 3K36 · UniProt Q3S340
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.