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The crystal structure of a broadly-reactive human anti-hemagglutinin stalk antibody (70-1F02) in complex with H5 hemagglutinin

Analyse The crystal structure of a broadly-reactive human anti-hemagglutinin stalk… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B3M
Type: protein
Length: 5,542 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1; Hemagglutinin HA2; 70-1F02 Fab heavy chain; 70-1F02 Fab light chain
UniProt: Q5EP31, A0A182DWE1
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, G, K, Q, S	Hemagglutinin HA1	protein	321	6% helix, 37% strand	Q5EP31
B	Hemagglutinin HA2	protein	174	57% helix, 10% strand	A0A182DWE1
C, I, M, O, V, Y	70-1F02 Fab heavy chain	protein	214	4% helix, 40% strand	—
F, H, L, R, T	Hemagglutinin HA2	protein	175	57% helix, 10% strand	A0A182DWE1
P	70-1F02 Fab light chain	protein	213	5% helix, 48% strand	—
U, J, D, W, N	70-1F02 Fab light chain	protein	214	5% helix, 48% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, C, B, D, E, G, K, L, R, I, M, O, Q, Y, S, V, F
MAN · alpha-D-mannopyranose · sugar · 17 copies · chains C, I, M, O, Y, V
BMA · beta-D-mannopyranose · sugar · 4 copies · chains M, Y, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	175	0.83	0.98	20	empty
2	824	0.83	0.86	113	empty
3	213	0.82	0.95	26	empty
4	226	0.82	0.95	27	empty
5	168	0.81	0.97	23	empty

Interfaces

54 interfaces between chains.

A–B · 2767 Å² buried · 33 hydrogen bonds · protein-protein
H–K · 2759 Å² buried · 34 hydrogen bonds · protein-protein
Q–R · 2754 Å² buried · 35 hydrogen bonds · protein-protein
G–L · 2742 Å² buried · 34 hydrogen bonds · protein-protein
S–T · 2734 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 60 disulfide, 31 glycan (disulfide, N-glycosylation, glycosylation, glycation).

Compared structures

6B3M · The crystal structure of a broadly-reactive human anti-hemagglutinin stalk antibody… · 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 Q5EP31
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Elsewhere: RCSB PDB 6B3M · PDBe 6B3M · UniProt Q5EP31 · UniProt A0A182DWE1

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