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The crystal structure of hemagglutinin form A/CHICKEN/NEW YORK/14677- 13/1998

Analyse The crystal structure of hemagglutinin form A/CHICKEN/NEW YORK/14677- 13/1998 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WSR
Type: protein
Length: 2,915 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: Q0A3A5
Ligands: NAG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 26% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	483	26% helix, 32% strand	Q0A3A5
B, C	Hemagglutinin	protein	482	25% helix, 32% strand	Q0A3A5
E	Hemagglutinin	protein	489	26% helix, 31% strand	Q0A3A5
D	Hemagglutinin	protein	498	26% helix, 31% strand	Q0A3A5
F	Hemagglutinin	protein	481	26% helix, 32% strand	Q0A3A5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C, F, D, E

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.81	0.90	55	empty
2	519	0.80	0.87	66	empty
3	808	0.78	0.81	62	empty
4	549	0.76	0.83	57	empty
5	598	0.73	0.80	78	empty

Interfaces

8 interfaces between chains.

E–F · 2213 Å² buried · 28 hydrogen bonds · protein-protein
E–D · 2168 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 2145 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2062 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 2054 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide, 13 glycan (disulfide, N-glycosylation).

Compared structures

4WSR · The crystal structure of hemagglutinin form A/chicken/New York/14677-13/1998 · 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 Q0A3A5
Elsewhere: RCSB PDB 4WSR · PDBe 4WSR · UniProt Q0A3A5

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