MolNFT v1 · #137814 · protein

A/TEXAS/50/2012(H3N2) influenza hemagglutinin in complex with K03.12 Fab

5W08 · Hemagglutinin HA1: “A/TEXAS/50/2012(H3N2) influenza hemagglutinin in complex with K03.12 Fab”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.76). MolNFT v1 #137814 on GenesisL1: 3D structure, binding sites…

PDB: 5W08
Type: protein
Length: 4,324 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1; K03.12 antibody heavy chain; K03.12 antibody light chain
UniProt: R4L1D1, S6C4S0, Q6IPQ0
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 10 distinct chains · 7% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Hemagglutinin HA1	protein	272	11% helix, 37% strand	R4L1D1
B, F	Hemagglutinin HA1	protein	274	11% helix, 35% strand	R4L1D1
D, E	Hemagglutinin HA1	protein	273	11% helix, 36% strand	R4L1D1
G	K03.12 antibody heavy chain	protein	236	5% helix, 51% strand	S6C4S0
H	K03.12 antibody light chain	protein	212	7% helix, 50% strand	Q6IPQ0
I	K03.12 antibody heavy chain	protein	238	5% helix, 51% strand	S6C4S0
J	K03.12 antibody light chain	protein	213	7% helix, 49% strand	Q6IPQ0
K, M, O, Q	K03.12 antibody heavy chain	protein	235	6% helix, 51% strand	S6C4S0
L	K03.12 antibody light chain	protein	211	7% helix, 48% strand	Q6IPQ0
N, P, R	K03.12 antibody light chain	protein	212	5% helix, 50% strand	Q6IPQ0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, C, D, E, F, O
BMA · beta-D-mannopyranose · sugar · 5 copies
GOL · Glycerol · additive · chains I, J

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1090	0.76	0.78	73	empty
2	768	0.69	0.76	64	empty
3	647	0.66	0.75	64	empty
4	624	0.65	0.75	64	empty
5	528	0.64	0.76	47	empty

Interfaces

27 interfaces between chains.

G–H · 1717 Å² buried · 11 hydrogen bonds · protein-protein
I–J · 1693 Å² buried · 10 hydrogen bonds · protein-protein
Q–R · 1677 Å² buried · 14 hydrogen bonds · protein-protein
K–L · 1662 Å² buried · 11 hydrogen bonds · protein-protein
M–N · 1626 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 50 disulfide, 25 glycan (disulfide, N-glycosylation).

Compared structures

5W08 · A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab · 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 R4L1D1
Every structure of UniProt S6C4S0
Every structure of UniProt Q6IPQ0
Elsewhere: RCSB PDB 5W08 · PDBe 5W08 · UniProt R4L1D1 · UniProt S6C4S0 · UniProt Q6IPQ0

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