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Influenza B/BRISBANE/60/2008 hemagglutinin Fab CR8059 complex

Analyse Influenza B/BRISBANE/60/2008 hemagglutinin Fab CR8059 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FQK
Type: protein
Length: 1,821 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1; Hemagglutinin HA2; Antibody CR8059 heavy chain; Antibody CR8059 light…
UniProt: C0LT38
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 7 distinct chains · 15% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Hemagglutinin HA1	protein	337	8% helix, 30% strand	C0LT38
B	Hemagglutinin HA2	protein	139	47% helix, 10% strand	C0LT38
D	Hemagglutinin HA2	protein	140	47% helix, 10% strand	C0LT38
E	Antibody CR8059 heavy chain	protein	220	7% helix, 50% strand	—
F	Antibody CR8059 light chain	protein	213	8% helix, 49% strand	—
H	Antibody CR8059 heavy chain	protein	221	7% helix, 50% strand	—
L	Antibody CR8059 light chain	protein	214	8% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C
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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.71	0.76	77	empty
2	932	0.71	0.75	78	empty
3	137	0.66	0.88	29	empty
4	116	0.66	0.89	29	empty
5	174	0.55	0.80	39	empty

Interfaces

8 interfaces between chains.

C–D · 2406 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2367 Å² buried · 25 hydrogen bonds · protein-protein
H–L · 1838 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1755 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 687 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

4FQK · Influenza B/Brisbane/60/2008 hemagglutinin Fab CR8059 complex · the same entry in another collection · chain H against H, 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 C0LT38
Elsewhere: RCSB PDB 4FQK · PDBe 4FQK · UniProt C0LT38

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