SMTL ID : 5dqd.1

Structure of S55-5 Fab in complex with lipid A carbohydrate backbone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GN1- GN4: 2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GN1-GN4.1: 13 residues within 4Å: Chain A: R.100 Chain B: G.33, I.51, S.52, R.53, G.54, G.55, S.56, Y.57, H.99, G.105, T.106, N.107 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.52, B:G.54, B:G.55, B:S.56, B:I.51, B:H.99, B:N.107, B:N.107 Water bridges: B:G.54, B:S.56, B:S.56, B:G.33, B:R.53, B:L.102, B:G.105, B:G.105, A:R.100 Salt bridges: B:H.99, A:R.100

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: T.101, F.102 Chain B: E.46, W.47 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain B: R.104 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haji-Ghassemi, O. et al., Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from unrelated V-genes. J.Biol.Chem. (2015)

Release Date

2016-03-09

Peptides

S55-5 Fab (IgG1 kappa) light chain: A
S55-5 Fab (IgG1) heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

S55-5 Fab (IgG1 kappa) light chain

S55-5 Fab (IgG1) heavy chain

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