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A subtype N10 neuraminidase-like protein of A/LITTLE yellow-shouldered BAT/GUATEMALA/060/2010
Analyse A subtype N10 neuraminidase-like protein of A/LITTLE yellow-shouldered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GDJ
- Type
- protein
- Length
- 1,266 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- H6QM95
- Ligands
- NAG, FUL, FUC, CA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase | protein | 317 | 2% helix, 51% strand | H6QM95 |
| B | Neuraminidase | protein | 321 | 2% helix, 52% strand | H6QM95 |
| C | Neuraminidase | protein | 314 | 2% helix, 52% strand | H6QM95 |
| D | Neuraminidase | protein | 314 | 2% helix, 52% strand | H6QM95 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains B, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.70 | 0.74 | 104 | NAG, FUC |
| 2 | 244 | 0.52 | 0.76 | 39 | empty |
| 3 | 178 | 0.49 | 0.77 | 29 | empty |
| 4 | 134 | 0.47 | 0.78 | 29 | empty |
| 5 | 154 | 0.45 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–C · 658 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 590 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 314 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4GDJ · A subtype N10 neuraminidase-like protein of A/little yellow-shouldered… · 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 H6QM95
- Elsewhere: RCSB PDB 4GDJ · PDBe 4GDJ · UniProt H6QM95
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