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Crystal structure of a subtype N11 neuraminidase-like protein of A/FLAT-faced BAT/PERU/033/2010 (H18N11)
Analyse Crystal structure of a subtype N11 neuraminidase-like protein of A/FLAT-faced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3Y
- Type
- protein
- Length
- 1,417 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- Ligands
- NAG, BMA, MAN, FUC, CA
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Neuraminidase | protein | 354 | 3% helix, 48% strand | — |
| C | Neuraminidase | protein | 355 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, B, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- 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
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.72 | 0.81 | 73 | empty |
| 2 | 325 | 0.70 | 0.83 | 48 | empty |
| 3 | 545 | 0.68 | 0.78 | 67 | empty |
| 4 | 330 | 0.62 | 0.79 | 48 | empty |
| 5 | 73 | 0.49 | 0.83 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1293 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1204 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 968 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 933 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4K3Y · Crystal structure of a subtype N11 neuraminidase-like protein of A/flat-faced… · 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 4K3Y · PDBe 4K3Y
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