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Crystal structure of human monoclonal antibody H3V-47 in complex with influenza virus hemagglutinin from A/MINNESOTA/11/2010 (H3N2)

Analyse Crystal structure of human monoclonal antibody H3V-47 in complex with influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W42
Type: protein
Length: 932 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin; Fab H3V-47 heavy chain; Fab H3V-47 light chain
UniProt: I0AXC3, Q6N089, Q8TCD0
Ligands: NAG, MAN, BMA, ZN
Pockets: 13 · best druggability 0.62

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	319	9% helix, 39% strand	I0AXC3
B	Hemagglutinin	protein	174	49% helix, 14% strand	I0AXC3
H	Fab H3V-47 heavy chain	protein	227	7% helix, 47% strand	Q6N089
L	Fab H3V-47 light chain	protein	212	5% helix, 53% strand	Q8TCD0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 9 copies
BMA · beta-D-mannopyranose · sugar · 4 copies
ZN · Zinc ion · metal · chains H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	243	0.62	0.81	29	empty
2	213	0.58	0.80	33	empty
3	66	0.58	0.89	18	empty
4	57	0.56	0.90	19	empty
5	214	0.49	0.75	31	empty

Interfaces

4 interfaces between chains.

A–B · 3081 Å² buried · 50 hydrogen bonds · protein-protein
H–L · 1642 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 701 Å² buried · 11 hydrogen bonds · protein-protein
A–L · 463 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5W42 · Crystal structure of human monoclonal antibody H3v-47 in complex with influenza virus… · 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 I0AXC3
Every structure of UniProt Q6N089
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 5W42 · PDBe 5W42 · UniProt I0AXC3 · UniProt Q6N089 · UniProt Q8TCD0

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