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Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin

Analyse Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NM8
Type: protein
Length: 2,757 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Antibody CR8043, light chain; Antibody…
UniProt: Q91MA7, P0DOX7, Q6N089
Ligands: NAG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Hemagglutinin HA1 chain	protein	318	10% helix, 41% strand	Q91MA7
B	Hemagglutinin HA2 chain	protein	172	52% helix, 15% strand	Q91MA7
D, F	Hemagglutinin HA2 chain	protein	171	56% helix, 13% strand	Q91MA7
E	Hemagglutinin HA1 chain	protein	317	10% helix, 42% strand	Q91MA7
L, M, N	Antibody CR8043, light chain	protein	217	5% helix, 52% strand	P0DOX7
H	Antibody CR8043, heavy chain	protein	215	8% helix, 52% strand	Q6N089
I	Antibody CR8043, heavy chain	protein	211	7% helix, 52% strand	Q6N089
J	Antibody CR8043, heavy chain	protein	213	7% helix, 51% strand	Q6N089

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, E, F, D

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	961	0.87	0.89	42	empty
2	232	0.84	0.96	29	empty
3	301	0.75	0.87	24	empty
4	317	0.74	0.86	24	empty
5	302	0.73	0.85	24	empty

Interfaces

27 interfaces between chains.

E–F · 2928 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 2892 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 2878 Å² buried · 45 hydrogen bonds · protein-protein
L–H · 1848 Å² buried · 13 hydrogen bonds · protein-protein
N–J · 1845 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide, 14 glycan (disulfide, N-glycosylation).

Compared structures

4NM8 · Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza… · the same entry in another collection · chain J against J, 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 Q91MA7
Every structure of UniProt P0DOX7
Every structure of UniProt Q6N089
Elsewhere: RCSB PDB 4NM8 · PDBe 4NM8 · UniProt Q91MA7 · UniProt P0DOX7 · UniProt Q6N089

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