MolNFT v1 · #124978 · protein
Crystal structure of a hpiv haemagglutinin-neuraminidase-inhibitor complex
5KV8 · Hemagglutinin-neuraminidase: “Crystal structure of a hpiv haemagglutinin-neuraminidase-inhibitor complex”. X-ray diffraction, 6 ligands (6Y6, NDG, BMA), 11 pockets (best druggability 0.65). MolNFT v1 #124978 on GenesisL1: 3D…
- PDB
- 5KV8
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase
- EC
- 3.2.1.18
- UniProt
- G8G134
- Ligands
- 6Y6, NDG, BMA, MAN, CA, SO4
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 430 | 6% helix, 45% strand | G8G134 |
| B | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 424 | 5% helix, 45% strand | G8G134 |
Ligands and binding sites
- 6Y6 · 2,6-anhydro-3,4,5-trideoxy-4-[4-(methoxymethyl)-1H-1,2, 3-triazol-1-yl]-5-[(2-methylpropanoyl)amino]-D-glycero-D-galacto -non-2-enonic acid · ligand · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.65 | 0.80 | 31 | 6Y6 |
| 2 | 349 | 0.65 | 0.80 | 32 | 6Y6 |
| 3 | 158 | 0.59 | 0.82 | 25 | empty |
| 4 | 284 | 0.57 | 0.77 | 45 | GOL |
| 5 | 163 | 0.55 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1793 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5KV8 · Crystal structure of a hPIV haemagglutinin-neuraminidase-inhibitor complex · 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 G8G134
- Elsewhere: RCSB PDB 5KV8 · PDBe 5KV8 · UniProt G8G134
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