SMTL ID : 3e6j.1

Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL-FUC.1: 14 residues within 4Å: Chain A: H.48, Y.70, S.73, D.94, T.97, F.118, C.120, A.141, D.143, Q.144, Y.165, F.167, W.195 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.97, A:Q.144, A:D.143, A:Q.144, A:D.94 Water bridges: A:Y.165, A:D.94, A:D.94, A:D.94 Hydrophobic interactions: A:Y.70

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: L.103, P.104, S.105, R.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.105 Water bridges: A:S.105, A:R.129, A:R.129 Salt bridges: A:R.129 SO4.3: 4 residues within 4Å: Chain A: W.195, G.197 Ligands: NAG-GAL-FUC.1, NAG-GAL-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.195 SO4.4: 1 residues within 4Å: Chain A: R.30 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.30 SO4.5: 4 residues within 4Å: Chain A: D.156, S.159, H.188 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.159 Salt bridges: A:H.188 SO4.6: 1 residues within 4Å: Chain A: R.157 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.157, A:R.157 Salt bridges: A:R.157

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: N.183, W.184, D.187, H.188 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.183, A:D.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, B.W. et al., Antigen recognition by variable lymphocyte receptors. Science (2008)

Release Date

2008-10-07

Peptides

Variable lymphocyte receptor diversity region: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Variable lymphocyte receptor diversity region