Research workbench
N2 neuraminidase D151G mutant of A/TANZANIA/205/2010 H3N2 in complex with avian sialic acid receptor
Analyse N2 neuraminidase D151G mutant of A/TANZANIA/205/2010 H3N2 in complex with avian… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZW
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- Ligands
- NAG, MAN, SIA, BMA, GAL, FUC, CA
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase | protein | 388 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains B, C, D, A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, C, D, A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · chains D
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.81 | 0.82 | 113 | empty |
| 2 | 318 | 0.60 | 0.78 | 44 | GAL, SIA |
| 3 | 313 | 0.60 | 0.78 | 42 | SIA |
| 4 | 194 | 0.57 | 0.80 | 37 | empty |
| 5 | 280 | 0.57 | 0.78 | 38 | GAL, SIA |
Interfaces
4 interfaces between chains.
- A–B · 1699 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1695 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1692 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1689 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 4GZW · N2 neuraminidase D151G mutant of A/Tanzania/205/2010 H3N2 in complex with avian sialic… · 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
- Elsewhere: RCSB PDB 4GZW · PDBe 4GZW
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