MolNFT v1 · #176190 · protein

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/DUCK northern CHINA/22/2017 (H5N6)

7DEA: “Structure of an avian influenza H5 hemagglutinin from the influenza virus A/DUCK northern CHINA/22/2017 (H5N6)”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.83). MolNFT v1 #176190 on GenesisL1: 3D structure…

PDB: 7DEA
Type: protein
Length: 1,470 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: A0A6M2RI35
Ligands: NAG
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, C	Hemagglutinin	protein	319	9% helix, 41% strand	—
F, D, B	Hemagglutinin	protein	171	57% helix, 13% strand	A0A6M2RI35

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains E, C, A

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	462	0.83	0.90	62	empty
2	453	0.79	0.87	58	empty
3	53	0.71	0.98	15	empty
4	312	0.65	0.81	42	empty
5	283	0.62	0.80	49	empty

Interfaces

15 interfaces between chains.

C–D · 2482 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2474 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 2432 Å² buried · 28 hydrogen bonds · protein-protein
D–B · 1292 Å² buried · 10 hydrogen bonds · protein-protein
F–D · 1292 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

7DEA · Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck Northern… · 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 A0A6M2RI35
Elsewhere: RCSB PDB 7DEA · PDBe 7DEA · UniProt A0A6M2RI35

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