Research workbench
Structure of a neuraminidase-like protein from A/BAT/GUATEMALA/164/2009
Analyse Structure of a neuraminidase-like protein from A/BAT/GUATEMALA/164/2009 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GEZ
- Type
- protein
- Length
- 4,377 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- H6QM85
- Ligands
- NAG, FUC, FUL, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, L | Neuraminidase | protein | 365 | 3% helix, 45% strand | H6QM85 |
| J | Neuraminidase | protein | 363 | 2% helix, 47% strand | H6QM85 |
| K | Neuraminidase | protein | 364 | 3% helix, 45% strand | H6QM85 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, E, F, I, C, D, G, H, J, K, L
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, E, I, D
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains B, F
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.79 | 0.96 | 34 | empty |
| 2 | 149 | 0.79 | 0.95 | 28 | empty |
| 3 | 130 | 0.78 | 0.96 | 25 | empty |
| 4 | 133 | 0.78 | 0.96 | 33 | empty |
| 5 | 130 | 0.78 | 0.96 | 32 | empty |
Interfaces
23 interfaces between chains.
- I–L · 1576 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 1576 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1576 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1570 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1560 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 4GEZ · Structure of a neuraminidase-like protein from A/bat/Guatemala/164/2009 · 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 4GEZ · PDBe 4GEZ · UniProt H6QM85
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