TABLE 3.

Hydrogen bond interactions between mAbs A6 and S1–15 to lipid A BBP and between S1–15 and oligonucleotide ligand

Lipid A numbering scheme is given in Fig. 2A.The distance cutoff for hydrogen bond assignment was 3.3 Å, except for charged residue interactions where the distance cutoff was 3.9 Å. Asterisk indicates charged residue interaction.

Antibody and PDB code	Antigen		Antibody		CDR	Distance
	Residue	Atom(s)	Residue	Atom
						Å
A6 4ODV	GlcN4P	O6	His(H)-100C	NE2	H3	3.04
		O5	Asn(H)-98	ND2	H3	3.16
		4PO4	Tyr(H)-96	OH	H3	2.68
			Lys(L)-53	NZ	L2	3.33*
			Tyr(L)-49	OH	L2	2.46
	GlcN1P	O5	Tyr(H)-32	OH	H1	3.15
		1PO4	Tyr(H)-32	OH	H1	2.24
			Arg(H)-100A	NE	H3	3.34*
			Arg(H)-100A	NH2	H3	2.87*
			Arg(L)-30	NH1	L1	2.41*
			Arg(L)-30	NH2	L1	2.57*
S1–15 4ODT	GlcN4P	O6	Ala(H)-33	N	H1	2.95
			Arg(H)-96	O	H3	2.85
		4PO4	Arg(H)-52	NE	H2	2.81*
			Arg(H)-52	NH2	H2	2.70*
			Arg(H)-96	NH1	H3	3.09*
	GlcN1P	O5	Ala(H)-98	N	H3	3.06
		1PO4	Tyr(H)-32	OH	H1	2.62
			Tyr(H)-100B	OH	H3	2.52
S1–15 4Z8F	dT chain E	3′PO4	Arg(H)-94	NH1	H3	2.96*
			Arg(H)-94	NH2	H3	2.69*
			Tyr(H)-100B	OH	H3	2.68
			Tyr(H)-102	OH	H3	3.12
			Arg(L)-55	NH2	L2	2.71*
		O2	Thr(H)-28	N	H1	2.85
		N3	Thr(H)-28	OG1	H1	2.88
	dT chain A	5′PO4	Arg(H)-50	NH1	H3	2.39*
			Arg(H)-50	NH1	H3	2.91*
			Arg(H)-52	NE	H3	2.92*
			Arg(H)-52	NH2	H3	2.87*
			Arg(H)-96	NH1	H3	3.05*
			Arg(H)-96	NH2	H3	2.93*
		O5	Asn(H)-53	ND2	H2	2.99
		O2	Ser(H)-52	OG	H2	3.06a

^a Poor electron density was observed for the terminal thymidine of chain A, and this hydrogen bond therefore cannot be assigned with confidence.