SMTL ID : 9g76.1

Crystal structure of ASGPR with bound GalNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.70, D.97, E.107, D.108 Ligands: GOL.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.70, A:D.70, A:D.97, A:E.107, H2O.1 CA.2: 7 residues within 4Å: Chain A: Q.94, D.96, E.107, N.119, D.120 Ligands: A2G.5, NGA.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.96, A:E.107, A:D.120, A:D.120 CA.3: 3 residues within 4Å: Chain A: V.45, E.51, E.132 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, A:E.51, A:E.132, A:E.132, H2O.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.70, G.73, W.75 Ligands: CA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.73, A:G.73

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.5: 12 residues within 4Å: Chain A: R.91, Q.94, D.96, W.98, E.107, H.111, N.119, D.120, D.121, Y.127 Ligands: CA.2, NGA.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.91, A:R.91, A:Q.94, A:N.119, A:N.119, A:D.121 Water bridges: A:W.98, A:D.121, A:R.125

1 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.6: 12 residues within 4Å: Chain A: R.91, Q.94, D.96, W.98, E.107, H.111, N.119, D.120, D.121, Y.127 Ligands: CA.2, A2G.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.91, A:R.91, A:Q.94, A:N.119, A:N.119, A:D.121 Water bridges: A:W.98, A:D.121, A:R.125 Salt bridges: A:R.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofmeister, A. et al., Trivalent siRNA-Conjugates with Guanosine as ASGPR-Binder Show Potent Knock-Down In Vivo. J.Med.Chem. (2025)

Release Date

2025-03-19

Peptides

Asialoglycoprotein receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Asialoglycoprotein receptor 1

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