Research workbench
Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir
Analyse Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TIA
- 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
- LNV, NAG, BMA, MAN, CA
- Pockets
- 13 · 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
- LNV · 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-D-glycero-D-galacto-non-2-enonic acid · 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
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.78 | 0.82 | 83 | empty |
| 2 | 272 | 0.63 | 0.81 | 46 | LNV |
| 3 | 274 | 0.63 | 0.81 | 46 | LNV |
| 4 | 259 | 0.62 | 0.81 | 37 | LNV |
| 5 | 264 | 0.62 | 0.80 | 45 | LNV |
Interfaces
4 interfaces between chains.
- A–D · 1686 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1683 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1681 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1668 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 3TIA · Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir · 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 3TIA · PDBe 3TIA · UniProt Q194T1
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