Research workbench
Wild-type influenza N2 neuraminidase covalent complex with 3-fluoro- NEU5AC
Analyse Wild-type influenza N2 neuraminidase covalent complex with 3-fluoro- NEU5AC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H52
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- Q194T1
- Ligands
- FSI, NAG, BMA, MAN, CA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase | protein | 388 | 4% helix, 48% strand | Q194T1 |
Ligands and binding sites
- FSI · 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.63 | 0.80 | 42 | FSI |
| 2 | 361 | 0.62 | 0.78 | 45 | FSI |
| 3 | 161 | 0.56 | 0.81 | 28 | empty |
| 4 | 209 | 0.56 | 0.79 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1678 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 4H52 · Wild-type influenza N2 neuraminidase covalent complex with 3-fluoro-Neu5Ac · 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 Q194T1
- Elsewhere: RCSB PDB 4H52 · PDBe 4H52 · UniProt Q194T1
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