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A subtype N10 neuraminidase-like protein of A/LITTLE yellow-shouldered BAT/GUATEMALA/164/2009
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
- 4GDI
- Type
- protein
- Length
- 2,202 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- H6QM85
- Ligands
- NAG, FUC, FUL, BMA, MAN, CA, NO3
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Neuraminidase | protein | 367 | 2% helix, 47% strand | H6QM85 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains A, B, C, D, E, F
- FUL · beta-L-fucopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 11 copies · chains A, B, C, D, E, F
- NO3 · Nitrate ion · ion · 14 copies · chains A, B, C, E, D, F
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.76 | 0.81 | 56 | empty |
| 2 | 263 | 0.73 | 0.87 | 38 | GOL |
| 3 | 700 | 0.71 | 0.78 | 73 | CA, NO3 |
| 4 | 260 | 0.70 | 0.85 | 46 | GOL, NO3 |
| 5 | 303 | 0.67 | 0.82 | 53 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1594 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1589 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1571 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1523 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 358 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 4GDI · 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 H6QM85
- Elsewhere: RCSB PDB 4GDI · PDBe 4GDI · UniProt H6QM85
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