MolNFT v1 · #104851 · protein
Neuraminidase N5 binds lsta at the second sia binding site
4QN5: “Neuraminidase N5 binds lsta at the second sia binding site”. X-ray diffraction, 4 ligands (NAG, SIA, GAL), 3 pockets (best druggability 0.70). MolNFT v1 #104851 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QN5
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- Q20UH7
- Ligands
- NAG, SIA, GAL, CA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase | protein | 394 | 4% helix, 46% strand | Q20UH7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.70 | 0.80 | 53 | SIA |
| 2 | 273 | 0.64 | 0.82 | 44 | SIA |
| 3 | 133 | 0.41 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4QN5 · Neuraminidase N5 binds LSTa at the second SIA binding site · the same entry in another collection · chain B against B, 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 Q20UH7
- Elsewhere: RCSB PDB 4QN5 · PDBe 4QN5 · UniProt Q20UH7
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