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Structure of influenza haemagglutinin in complex with an inhibitor of membrane fusion

Analyse Structure of influenza haemagglutinin in complex with an inhibitor of membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EYM
Type: protein
Length: 1,469 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
UniProt: P03437
Ligands: EYK
Pockets: 18 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin HA1 chain	protein	317	10% helix, 39% strand	P03437
B, D, F	Hemagglutinin HA2 chain	protein	172	54% helix, 15% strand	P03437
C, E	Hemagglutinin HA1 chain	protein	318	10% helix, 41% strand	P03437

Ligands and binding sites

EYK · 2-tert-butylbenzene-1,4-diol · ligand · 3 copies · chains B, F, D

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

Pockets

18 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	1029	0.87	0.88	111	empty
2	265	0.84	0.95	32	empty
3	342	0.75	0.86	32	EYK
4	331	0.75	0.86	29	EYK
5	81	0.73	0.96	23	empty

Interfaces

15 interfaces between chains.

E–F · 3046 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 2983 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 2970 Å² buried · 44 hydrogen bonds · protein-protein
B–D · 1500 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 1499 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

3EYM · Structure of Influenza Haemagglutinin in complex with an inhibitor of membrane fusion · 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 3EYM · PDBe 3EYM · UniProt P03437

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