MolNFT v1 · #79951 · protein
Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with zanamivir
3TIC: “Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with zanamivir”. X-ray diffraction, 5 ligands (ZMR, NAG, BMA), 14 pockets (best druggability 0.78). MolNFT v1 #79951 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3TIC
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- Q194T1
- Ligands
- ZMR, NAG, BMA, MAN, CA
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase | protein | 388 | 3% helix, 48% strand | Q194T1 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, D, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains D, A, B, C
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.78 | 0.82 | 79 | empty |
| 2 | 259 | 0.64 | 0.82 | 45 | ZMR |
| 3 | 253 | 0.63 | 0.82 | 43 | ZMR |
| 4 | 246 | 0.61 | 0.81 | 37 | ZMR |
| 5 | 181 | 0.57 | 0.81 | 32 | ZMR |
Interfaces
4 interfaces between chains.
- C–D · 1682 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1678 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1676 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1673 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 3TIC · Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with zanamivir · 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 Q194T1
- Elsewhere: RCSB PDB 3TIC · PDBe 3TIC · UniProt Q194T1
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