MolNFT v1 · #142331 · protein

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

6A0Z · HEMAGGLUTININ,ENVELOPE glycoprotein: “Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, ha head region”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.61). MolNFT v1…

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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