SMTL ID : 8dvn.1

Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: W.401, C.403, V.408, N.410, T.412, S.418, V.421 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: D.44, N.45, F.61, N.63, S.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.44, A:N.45

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain A: A.295, D.296, N.297 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 5 residues within 4Å: Chain A: Y.215, N.230, T.232, N.236 Ligands: NAG.5 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.236 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: L.209, D.249, I.250 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.209, A:I.250 CA.7: 4 residues within 4Å: Chain A: T.95, G.96, N.98, S.120 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.95, A:S.120 CA.8: 3 residues within 4Å: Chain A: D.389, L.390, I.433 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.389, A:I.433 CA.9: 3 residues within 4Å: Chain A: L.521, D.561, I.562 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.561, A:I.562

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thakur, A.K. et al., Synthetic Multivalent Disulfide-Constrained Peptide Agonists Potentiate Wnt1/ beta-Catenin Signaling via LRP6 Coreceptor Clustering. Acs Chem.Biol. (2023)

Release Date

2023-03-29

Peptides

Low-density lipoprotein receptor-related protein 6: A
E3.10 Disulfide constrained peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low-density lipoprotein receptor-related protein 6

E3.10 Disulfide constrained peptide

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