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Binding of influenza virus hemagglutinin to analogs of its cell- surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography

Analyse Binding of influenza virus hemagglutinin to analogs of its cell- surface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HGE
Type: protein
Length: 1,509 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin, (G135R), HA1 chain
UniProt: P03437
Ligands: MNA, NAG, BMA
Pockets: 19 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Hemagglutinin, (G135R), HA1 chain	protein	328	9% helix, 41% strand	P03437
B, D, F	Hemagglutinin, (G135R), HA1 chain	protein	175	53% helix, 15% strand	P03437

Ligands and binding sites

MNA · 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid · ligand · 3 copies · chains A, C, E
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, E, C, B, D, F
BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, A, C

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

Pockets

19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.87	0.88	112	empty
2	282	0.85	0.95	31	empty
3	1162	0.76	0.79	126	empty
4	709	0.74	0.80	69	empty
5	95	0.74	0.96	22	empty

Interfaces

15 interfaces between chains.

E–F · 3171 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 3138 Å² buried · 60 hydrogen bonds · protein-protein
C–D · 3042 Å² buried · 49 hydrogen bonds · protein-protein
B–F · 1579 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 1571 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

1HGE · Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic… · 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 P03437
Elsewhere: RCSB PDB 1HGE · PDBe 1HGE · UniProt P03437

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