MolNFT v1 · #124254 · protein

Crystal structure of multidonor HV1-18-class broadly neutralizing influenza a antibody 16.A.26 in complex with A/HONG KONG/1-4-MA21- 1/1968 (H3N2) hemagglutinin

5K9Q · Hemagglutinin HA1: “Crystal structure of multidonor HV1-18-class broadly neutralizing influenza a antibody 16.A.26 in complex…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #124254 on GenesisL1…

PDB: 5K9Q
Type: protein
Length: 5,582 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1; Hemagglutinin HA2; 16.A.26 heavy chain; 16.A.26 light chain
UniProt: Q91MA7
Ligands: NAG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 13 distinct chains · 25% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin HA1	protein	320	10% helix, 41% strand	Q91MA7
B	Hemagglutinin HA2	protein	168	55% helix, 14% strand	Q91MA7
C	Hemagglutinin HA1	protein	319	10% helix, 41% strand	Q91MA7
D	Hemagglutinin HA2	protein	169	54% helix, 14% strand	Q91MA7
E, M, O	Hemagglutinin HA1	protein	318	10% helix, 41% strand	Q91MA7
F	Hemagglutinin HA2	protein	168	55% helix, 14% strand	Q91MA7
G, J, S, U, X	16.A.26 heavy chain	protein	231	7% helix, 49% strand	—
H	16.A.26 heavy chain	protein	228	8% helix, 50% strand	—
I, K, L, T, V, Y	16.A.26 light chain	protein	214	7% helix, 50% strand	—
N	Hemagglutinin HA2	protein	169	56% helix, 14% strand	Q91MA7
P	Hemagglutinin HA2	protein	163	57% helix, 15% strand	Q91MA7
Q	Hemagglutinin HA1	protein	318	9% helix, 42% strand	Q91MA7
R	Hemagglutinin HA2	protein	167	55% helix, 14% strand	Q91MA7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, H, M, C, Q, T, D, G, Y, E, F, J, N, S, L, O, P, U, R, X

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	719	0.85	0.88	93	empty
2	724	0.83	0.87	83	empty
3	611	0.83	0.88	87	empty
4	494	0.83	0.90	43	empty
5	677	0.82	0.86	56	empty

Interfaces

74 interfaces between chains.

O–P · 2960 Å² buried · 47 hydrogen bonds · protein-protein
Q–R · 2941 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 2903 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 2899 Å² buried · 39 hydrogen bonds · protein-protein
E–F · 2891 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 65 disulfide, 36 glycan (disulfide, N-glycosylation).

Compared structures

5K9Q · Crystal structure of multidonor HV1-18-class broadly neutralizing Influenza A antibody… · 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 Q91MA7
Elsewhere: RCSB PDB 5K9Q · PDBe 5K9Q · UniProt Q91MA7

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