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Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G

Analyse Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JUG
Type: protein
Length: 2,950 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: Q9WFX3
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Hemagglutinin	protein	324	10% helix, 40% strand	Q9WFX3
B, H	Hemagglutinin	protein	170	52% helix, 12% strand	Q9WFX3
D	Hemagglutinin	protein	169	49% helix, 15% strand	Q9WFX3
F, L	Hemagglutinin	protein	165	51% helix, 13% strand	Q9WFX3
J	Hemagglutinin	protein	167	50% helix, 15% strand	Q9WFX3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, C, D, E, G, I, J, K
BMA · beta-D-mannopyranose · sugar · 2 copies

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	196	0.83	0.97	28	empty
2	197	0.83	0.97	25	empty
3	863	0.82	0.85	108	empty
4	460	0.78	0.86	73	empty
5	531	0.77	0.84	71	empty

Interfaces

33 interfaces between chains.

A–B · 2788 Å² buried · 48 hydrogen bonds · protein-protein
G–H · 2784 Å² buried · 45 hydrogen bonds · protein-protein
E–F · 2779 Å² buried · 46 hydrogen bonds · protein-protein
I–J · 2779 Å² buried · 51 hydrogen bonds · protein-protein
K–L · 2765 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

4JUG · Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G · 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 Q9WFX3
Elsewhere: RCSB PDB 4JUG · PDBe 4JUG · UniProt Q9WFX3

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