Research workbench
Crystal structure of 2009 pandemic H1N1 neuraminidase complexed with laninamivir
Analyse Crystal structure of 2009 pandemic H1N1 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
- 3TI3
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- C3W5S3
- Ligands
- LNV, NAG, CA
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase | protein | 387 | 3% helix, 46% strand | C3W5S3 |
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 · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.65 | 0.83 | 40 | LNV, ACT |
| 2 | 282 | 0.63 | 0.81 | 39 | LNV, GOL |
| 3 | 198 | 0.57 | 0.80 | 27 | GOL |
| 4 | 117 | 0.39 | 0.74 | 23 | empty |
| 5 | 53 | 0.29 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1576 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3TI3 · Crystal structure of 2009 pandemic H1N1 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 C3W5S3
- Elsewhere: RCSB PDB 3TI3 · PDBe 3TI3 · UniProt C3W5S3
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