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Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, ha head region

Analyse Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6A0Z
Type: protein
Length: 706 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HEMAGGLUTININ,ENVELOPE glycoprotein; Antibody 13D4, Fab heavy chain; Antibody 13D4, Fab…
UniProt: Q45ZR9, M1E1E4
Ligands: NAG
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HEMAGGLUTININ,ENVELOPE glycoprotein	protein	270	11% helix, 39% strand	Q45ZR9, M1E1E4
H	Antibody 13D4, Fab heavy chain	protein	224	5% helix, 50% strand	—
L	Antibody 13D4, Fab light chain	protein	212	5% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	520	0.61	0.74	72	empty
2	145	0.45	0.76	24	empty
3	52	0.38	0.81	19	empty
4	72	0.34	0.76	17	empty
5	77	0.33	0.75	21	empty

Interfaces

3 interfaces between chains.

H–L · 1922 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 752 Å² buried · 18 hydrogen bonds · protein-protein
A–L · 249 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, cyclization).

Compared structures

6A0Z · Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza… · 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 Q45ZR9
Every structure of UniProt M1E1E4
Elsewhere: RCSB PDB 6A0Z · PDBe 6A0Z · UniProt Q45ZR9 · UniProt M1E1E4

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