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Crystal structure of the ivr-165 (H3N2) influenza virus hemagglutinin in complex with 3'-slnln
Analyse Crystal structure of the ivr-165 (H3N2) influenza virus hemagglutinin in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NSA
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- L0HR89
- Ligands
- NAG, MAN, BMA, GAL, SIA
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 41% strand | L0HR89 |
| B | Hemagglutinin HA2 chain | protein | 169 | 54% helix, 14% strand | L0HR89 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.56 | 0.89 | 20 | empty |
| 2 | 102 | 0.37 | 0.75 | 18 | empty |
| 3 | 56 | 0.29 | 0.75 | 17 | empty |
| 4 | 61 | 0.29 | 0.74 | 16 | SIA |
| 5 | 52 | 0.23 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2986 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NSA · Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with… · 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 L0HR89
- Elsewhere: RCSB PDB 6NSA · PDBe 6NSA · UniProt L0HR89
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