SMTL ID : 8oxd.1

Structure of the human LYVE-1 (lymphatic vessel endothelial receptor-1) hyaluronan binding domain bound with decasaccharide hyaluronan.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

1 x BDP- NAG- BDP- NAG- BDP- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-NAG-BDP-NAG-BDP-NAG.1: 12 residues within 4Å: Chain A: C.85, Y.87, I.97, N.103, K.105, C.106, G.107, K.108, L.114, I.115, W.116, K.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.85 Salt bridges: A:K.105

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 6 residues within 4Å: Chain A: R.37, L.64, G.65, N.130, S.132, D.133 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.37, A:N.130, A:S.132, A:D.133 Water bridges: A:D.133, A:T.134, A:T.134 NAG.3: 4 residues within 4Å: Chain A: N.53, E.56, V.120, S.121 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.120 Hydrogen bonds: A:N.53 Water bridges: A:L.25, A:L.25, A:N.53, A:T.55 NAG.4: 7 residues within 4Å: Chain A: C.36, I.38, A.80, S.81, N.137, C.139, I.140 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.38 Hydrogen bonds: A:N.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bano, F. et al., A novel sliding interaction with hyaluronan underlies the mode of action of LYVE-1, the receptor for leucocyte entry and trafficking in the lymphatics. To be published

Release Date

2024-11-13

Peptides

Lymphatic vessel endothelial hyaluronic acid receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lymphatic vessel endothelial hyaluronic acid receptor 1

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