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Crystal structure of a H5N1 influenza virus hemagglutinin at pH 7.0

Analyse Crystal structure of a H5N1 influenza virus hemagglutinin at pH 7.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PD6
Type: protein
Length: 491 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: Q1KHJ8
Ligands: NAG, SO4
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	491	24% helix, 28% strand	Q1KHJ8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
SO4 · Sulfate ion · ion · 11 copies · chains A
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	251	0.61	0.80	22	SO4
2	116	0.46	0.79	20	SO4
3	76	0.40	0.78	13	empty
4	116	0.39	0.75	24	GOL

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6PD6 · Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 7.0 · 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 Q1KHJ8
Elsewhere: RCSB PDB 6PD6 · PDBe 6PD6 · UniProt Q1KHJ8

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