MolNFT v1 · #93883 · protein

Crystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin

4HG4 · Hemagglutinin HA1: “Crystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #93883 on GenesisL1: 3D structure…

PDB: 4HG4
Type: protein
Length: 7,479 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1; Hemagglutinin HA2; Fab 2G1 heavy chain; Fab 2G1 light chain
UniProt: Q67085
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 24 distinct chains · 12% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Hemagglutinin HA1	protein	323	11% helix, 37% strand	Q67085
a	Hemagglutinin HA2	protein	171	50% helix, 9% strand	Q67085
B	Hemagglutinin HA1	protein	319	10% helix, 35% strand	Q67085
b	Hemagglutinin HA2	protein	167	53% helix, 6% strand	Q67085
C, D, F, G, I	Hemagglutinin HA1	protein	324	10% helix, 39% strand	Q67085
c, d, e, f, g, i	Hemagglutinin HA2	protein	172	53% helix, 12% strand	Q67085
H	Hemagglutinin HA1	protein	325	10% helix, 36% strand	Q67085
h	Hemagglutinin HA2	protein	167	51% helix, 13% strand	Q67085
J	Fab 2G1 heavy chain	protein	115	0% helix, 35% strand	—
K	Fab 2G1 light chain	protein	106	0% helix, 36% strand	—
L	Fab 2G1 heavy chain	protein	212	7% helix, 50% strand	—
M, O	Fab 2G1 light chain	protein	214	4% helix, 49% strand	—
N	Fab 2G1 heavy chain	protein	223	7% helix, 48% strand	—
P	Fab 2G1 heavy chain	protein	161	6% helix, 37% strand	—
Q	Fab 2G1 light chain	protein	157	0% helix, 39% strand	—
R	Fab 2G1 heavy chain	protein	214	4% helix, 49% strand	—
S, U	Fab 2G1 light chain	protein	211	2% helix, 43% strand	—
T	Fab 2G1 heavy chain	protein	213	3% helix, 44% strand	—
V	Fab 2G1 heavy chain	protein	117	0% helix, 49% strand	—
W	Fab 2G1 light chain	protein	105	0% helix, 44% strand	—
X	Fab 2G1 heavy chain	protein	164	4% helix, 40% strand	—
Y	Fab 2G1 light chain	protein	109	0% helix, 45% strand	—
Z	Fab 2G1 heavy chain	protein	167	4% helix, 43% strand	—
z	Fab 2G1 light chain	protein	119	0% helix, 38% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B, C, D, E, F, G, H, I
BMA · beta-D-mannopyranose · sugar · 2 copies

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	1067	0.86	0.87	128	empty
2	621	0.84	0.89	71	empty
3	1033	0.84	0.85	96	empty
4	960	0.84	0.85	89	empty
5	529	0.83	0.89	55	empty

Interfaces

79 interfaces between chains.

I–i · 2802 Å² buried · 40 hydrogen bonds · protein-protein
D–d · 2783 Å² buried · 31 hydrogen bonds · protein-protein
C–c · 2741 Å² buried · 35 hydrogen bonds · protein-protein
A–a · 2736 Å² buried · 34 hydrogen bonds · protein-protein
F–f · 2707 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 75 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

4HG4 · Crystal structure of Fab 2G1 in complex with a H2N2 influenza virus 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 Q67085
Elsewhere: RCSB PDB 4HG4 · PDBe 4HG4 · UniProt Q67085

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