Research workbench

Crystal structure of a H5N1 influenza virus hemagglutinin at pH 5.5

Analyse Crystal structure of a H5N1 influenza virus hemagglutinin at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PD3
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: 6 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	491	25% helix, 29% strand	Q1KHJ8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
SO4 · Sulfate ion · ion · 12 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

6 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	301	0.61	0.79	31	SO4
2	143	0.48	0.78	21	SO4
3	113	0.44	0.77	21	empty
4	83	0.39	0.78	21	empty
5	83	0.32	0.73	15	GOL

Modifications

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

Compared structures

6PD3 · Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 5.5 · 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 6PD3 · PDBe 6PD3 · UniProt Q1KHJ8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.