SMTL ID : 4odt.1

Fab Structure of lipid A-specific antibody S1-15 in complex with lipid A carbohydrate backbone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GP1- Z9M: 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GP1-Z9M.1: 12 residues within 4Å: Chain A: T.31, Y.32, A.33, R.52, N.56, R.100, H.101, R.102, G.103, A.104, P.105, Y.108 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.31, A:Y.32, A:Y.32, A:R.100, A:A.104, A:Y.108, A:A.33, A:R.50, A:N.56, A:H.101 Water bridges: A:R.100, A:R.100, A:R.52, A:H.101, A:R.102, A:R.102 Salt bridges: A:R.52, A:R.102

4 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 8 residues within 4Å: Chain A: Q.39, K.43 Chain B: Q.38, K.39, P.40, T.85, F.87, G.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.39 PG0.3: 5 residues within 4Å: Chain A: L.45, E.46 Chain B: F.98, G.99, G.100 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:F.98, A:G.44 PG0.4: 1 residues within 4Å: Chain B: S.63 No protein-ligand interaction detected (PLIP) PG0.5: 3 residues within 4Å: Chain B: K.142, D.143, W.163 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.142, B:K.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haji-Ghassemi, O. et al., Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA. J.Biol.Chem. (2015)

Release Date

2015-06-24

Peptides

S1-15 Fab (IgG2b) heavy chain: A
S1-15 Fab (IgG2b kappa) light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

S1-15 Fab (IgG2b) heavy chain

S1-15 Fab (IgG2b kappa) light chain

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