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Crystal structure of HA2 R106H mutant of H2 hemagglutinin, acidic pH form

Analyse Crystal structure of HA2 R106H mutant of H2 hemagglutinin, acidic pH form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QQO
Type: protein
Length: 1,482 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: C7S226
Ligands: NAG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Hemagglutinin	protein	322	7% helix, 38% strand	C7S226
B, D, F	Hemagglutinin	protein	172	53% helix, 12% strand	C7S226

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	288	0.86	0.96	32	empty
2	1143	0.84	0.85	114	empty
3	169	0.82	0.97	20	empty
4	259	0.78	0.90	33	empty
5	293	0.78	0.89	33	empty

Interfaces

15 interfaces between chains.

C–D · 2851 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 2810 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 2787 Å² buried · 39 hydrogen bonds · protein-protein
B–D · 1579 Å² buried · 15 hydrogen bonds · protein-protein
B–F · 1573 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

3QQO · Crystal structure of HA2 R106H mutant of H2 hemagglutinin, acidic pH form · 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 C7S226
Elsewhere: RCSB PDB 3QQO · PDBe 3QQO · UniProt C7S226

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