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Murine antibody that engages the influenza hemagglutinin receptor binding site

Analyse Murine antibody that engages the influenza hemagglutinin receptor binding site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JIX
Type: protein
Length: 931 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Fab light chain; Fab heavy chain
UniProt: A7Y8A6, G2TTT7
Ligands: NAG, BMA, MAN
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin HA1 chain	protein	323	10% helix, 37% strand	A7Y8A6
B	Hemagglutinin HA2 chain	protein	173	50% helix, 9% strand	G2TTT7
L	Fab light chain	protein	216	5% helix, 51% strand	—
H	Fab heavy chain	protein	219	4% helix, 48% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
BMA · beta-D-mannopyranose · sugar · 3 copies
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	111	0.78	0.98	27	empty
2	730	0.66	0.75	63	empty
3	121	0.49	0.80	19	empty
4	202	0.47	0.75	27	empty
5	92	0.43	0.79	20	empty

Interfaces

4 interfaces between chains.

A–B · 2902 Å² buried · 47 hydrogen bonds · protein-protein
L–H · 1854 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 720 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 675 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

7JIX · Murine antibody that engages the influenza hemagglutinin receptor binding site · 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 A7Y8A6
Every structure of UniProt G2TTT7
Elsewhere: RCSB PDB 7JIX · PDBe 7JIX · UniProt A7Y8A6 · UniProt G2TTT7

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