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Crystal structure of the haemagglutinin mutant (GLN226LEU, GLY228SER) from an H10N7 seal influenza virus isolated in germany with 2MM edta

Analyse Crystal structure of the haemagglutinin mutant (GLN226LEU, GLY228SER) from an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TWS
Type: protein
Length: 1,476 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin; Hemagglutinin HA2
UniProt: A0A0A7HR51
Ligands: NAG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, A, C	Hemagglutinin	protein	320	8% helix, 39% strand	A0A0A7HR51
H, B, D	Hemagglutinin HA2	protein	172	54% helix, 15% strand	A0A0A7HR51

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains H, A, G, B, C, D
EDO · 1,2-ethanediol · additive · 22 copies · chains G, H, D, A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	183	0.84	0.98	24	empty
2	1164	0.83	0.84	132	empty
3	84	0.74	0.96	16	EDO
4	78	0.74	0.97	18	EDO
5	74	0.72	0.96	16	EDO

Interfaces

15 interfaces between chains.

C–D · 3293 Å² buried · 47 hydrogen bonds · protein-protein
G–H · 3283 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 3225 Å² buried · 46 hydrogen bonds · protein-protein
H–B · 1486 Å² buried · 16 hydrogen bonds · protein-protein
H–D · 1471 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

6TWS · Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal… · the same entry in another collection · chain G against G, 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 A0A0A7HR51
Elsewhere: RCSB PDB 6TWS · PDBe 6TWS · UniProt A0A0A7HR51

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