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The structure of hemagglutinin from a H6N1 influenza virus (A/TAIWAN/2/2013)

Analyse The structure of hemagglutinin from a H6N1 influenza virus (A/TAIWAN/2/2013) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YY9
Type: protein
Length: 487 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HA1; HA2
Ligands: NAG, BMA
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HA1	protein	325	9% helix, 39% strand	—
B	HA2	protein	162	52% helix, 14% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
BMA · beta-D-mannopyranose · sugar

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.47	0.82	22	empty
2	87	0.46	0.81	15	empty

Interfaces

1 interface between chains.

A–B · 2731 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4YY9 · The structure of hemagglutinin from a H6N1 influenza virus (A/Taiwan/2/2013) · 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 4YY9 · PDBe 4YY9

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