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Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) influenza hemagglutinin

Analyse Crystal structure of broadly neutralizing antibody F045-092 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4O5I
Type: protein
Length: 5,574 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 6.501
Source: Homo sapiens; Influenza A virus
Molecule: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Fab F045-092 heavy chain; Fab F045-092…
UniProt: R9U684, S6C4S0, P0CG05
Ligands: NAG, BMA, MAN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · resolution 6.501 · 4 distinct chains · 17% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Hemagglutinin HA1 chain	protein	317	10% helix, 41% strand	R9U684
B, D, F, H, J, L	Hemagglutinin HA2 chain	protein	173	51% helix, 15% strand	R9U684
M, O, Q, S, U, W	Fab F045-092 heavy chain	protein	226	10% helix, 48% strand	S6C4S0
N, P, R, T, V, X	Fab F045-092 light chain	protein	213	8% helix, 51% strand	P0CG05

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, B, M, E, C, D, O, F, Q, G, H, S, K, I, J, U, L, W
BMA · beta-D-mannopyranose · sugar · 20 copies · chains B
MAN · alpha-D-mannopyranose · sugar · 11 copies · chains E, F

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	992	0.88	0.89	116	empty
2	1096	0.86	0.87	124	empty
3	329	0.86	0.95	34	empty
4	329	0.85	0.95	36	empty
5	912	0.75	0.79	88	empty

Interfaces

45 interfaces between chains.

K–L · 3033 Å² buried · 44 hydrogen bonds · protein-protein
I–J · 3028 Å² buried · 39 hydrogen bonds · protein-protein
E–F · 3023 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 3006 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 3004 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 66 disulfide, 47 glycan (disulfide, N-glycosylation).

Compared structures

4O5I · Crystal structure of broadly neutralizing antibody F045-092 in complex with… · 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 R9U684
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Every structure of UniProt P0CG05
Elsewhere: RCSB PDB 4O5I · PDBe 4O5I · UniProt R9U684 · UniProt S6C4S0 · UniProt P0CG05

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