Research workbench
Crystal structure of hemagglutinin of A/TAIWAN/2/2013 (H6N1) in complex with lstc
Analyse Crystal structure of hemagglutinin of A/TAIWAN/2/2013 (H6N1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BR6
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- Ligands
- NAG, MAN, GAL, SIA, BMA, FUC
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin HA1 chain | protein | 326 | 9% helix, 38% strand | — |
| B, D | Hemagglutinin HA2 chain | protein | 171 | 56% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.69 | 0.77 | 57 | empty |
| 2 | 167 | 0.44 | 0.75 | 23 | empty |
| 3 | 64 | 0.44 | 0.82 | 21 | empty |
| 4 | 76 | 0.42 | 0.80 | 20 | empty |
| 5 | 67 | 0.42 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2753 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2724 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 300 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5BR6 · Crystal structure of hemagglutinin of A/Taiwan/2/2013 (H6N1) in complex with LSTc · 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
- Elsewhere: RCSB PDB 5BR6 · PDBe 5BR6
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