SMTL ID : 8urf.1

Crystal Structure of human ASGR2 CRD (Carbohydrate Recognition Domain) bound to 8G8 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 12 residues within 4Å: Chain A: Q.160, S.162, S.176, S.177, T.178 Chain B: L.146, F.171, P.172, V.174, S.182, L.183, S.184 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.160, A:S.162, A:S.162, A:T.178, B:S.184 GOL.2: 7 residues within 4Å: Chain B: T.28, T.31, Y.32, R.100 Chain C: W.5, V.6, E.7 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:E.7, B:T.28, B:T.28, B:T.31, B:T.31, B:R.100 Water bridges: C:C.1, C:W.5 GOL.6: 7 residues within 4Å: Chain C: Q.87, D.89, W.91, E.100, N.112, D.113 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.87, C:D.89, C:N.112, C:N.112 Water bridges: C:E.100 GOL.7: 7 residues within 4Å: Chain C: W.42, Q.45, V.49, N.82, D.108, G.109, R.110 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.45, C:N.82, C:G.109 Water bridges: C:R.110 GOL.8: 3 residues within 4Å: Chain A: Y.32 Chain B: R.102 Chain C: E.43 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:E.43, C:E.43, A:Y.32, A:Y.32, B:R.102 Water bridges: A:Y.92, B:R.102

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain C: D.63, N.90, E.100, D.101 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.63, C:D.63, C:E.100, H2O.7, H2O.9 CA.4: 6 residues within 4Å: Chain C: Q.87, D.89, E.100, N.112, D.113 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.89, C:E.100, C:D.113, C:D.113 CA.5: 4 residues within 4Å: Chain C: V.38, N.40, E.44, E.125 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.44, C:E.44, C:E.125, C:E.125, H2O.9

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

CL.9: 1 residues within 4Å: Chain C: H.94 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Targeted protein degradation systems to enhance Wnt signaling. Elife (2024)

Release Date

2024-06-19

Peptides

8G8 Fab Light Chain: A
8G8 Fab Heavy Chain: B
Asialoglycoprotein receptor 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

8G8 Fab Light Chain

8G8 Fab Heavy Chain

Asialoglycoprotein receptor 2