MolNFT v1 · #101894 · protein

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

4O5I · Hemagglutinin HA1 chain: “Crystal structure of broadly neutralizing antibody F045-092 in complex with A/VICTORIA/361/2011 (H3N2)…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.88). MolNFT v1 #101894…

PDB: 4O5I
Type: protein
Length: 5,574 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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 · 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 B against B, 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
Every structure of UniProt S6C4S0
Every structure of UniProt P0CG05
Elsewhere: RCSB PDB 4O5I · PDBe 4O5I · UniProt R9U684 · UniProt S6C4S0 · UniProt P0CG05

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