MolNFT v1 · #93284 · protein

Crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin

4GXU · Hemagglutinin HA1 chain: “Crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.88). MolNFT v1 #93284 on GenesisL1: 3D structure…

PDB: 4GXU
Type: protein
Length: 4,804 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Antibody 1F1, heavy chain; Antibody…
UniProt: Q9WFX3
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 6 distinct chains · 14% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Hemagglutinin HA1 chain	protein	325	9% helix, 41% strand	Q9WFX3
B, D, F, H, J, L	Hemagglutinin HA2 chain	protein	171	57% helix, 15% strand	Q9WFX3
M, Q	Antibody 1F1, heavy chain	protein	228	5% helix, 50% strand	—
N, R	Antibody 1F1, light chain	protein	214	7% helix, 51% strand	—
O, S, U, W	Antibody 1F1, heavy chain	protein	125	5% helix, 49% strand	—
P, T, V, X	Antibody 1F1, light chain	protein	111	3% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, E, G, I, K, B, D, F, H, J, L
BMA · beta-D-mannopyranose · sugar · 6 copies · chains M, O, Q, S, U, W

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	1044	0.88	0.90	143	empty
2	499	0.87	0.93	78	empty
3	433	0.77	0.86	58	empty
4	1085	0.74	0.77	112	empty
5	567	0.72	0.80	51	empty

Interfaces

58 interfaces between chains.

C–D · 2858 Å² buried · 44 hydrogen bonds · protein-protein
I–J · 2830 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2810 Å² buried · 50 hydrogen bonds · protein-protein
K–L · 2792 Å² buried · 53 hydrogen bonds · protein-protein
G–H · 2773 Å² buried · 53 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 52 disulfide, 18 glycan, 12 modified (disulfide, N-glycosylation, cyclization).

Compared structures

4GXU · Crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin · 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 Q9WFX3
Elsewhere: RCSB PDB 4GXU · PDBe 4GXU · UniProt Q9WFX3

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