Research workbench
Crystal structure of the A/WYOMING/3/2003 (H3N2) influenza virus hemagglutinin in complex with 6'-sln
Analyse Crystal structure of the A/WYOMING/3/2003 (H3N2) influenza virus hemagglutinin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BKR
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A4GYF9, B4UPH9
- Ligands
- NAG, BMA, MAN, GAL, SIA
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 40% strand | A4GYF9 |
| B | Hemagglutinin HA2 chain | protein | 173 | 53% helix, 15% strand | B4UPH9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.53 | 0.78 | 39 | empty |
| 2 | 55 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3030 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6BKR · Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin in 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 A4GYF9
- Every structure of UniProt B4UPH9
- Elsewhere: RCSB PDB 6BKR · PDBe 6BKR · UniProt A4GYF9 · UniProt B4UPH9
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