SMTL ID : 8dvl.1

Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.18

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 3 residues within 4Å: Chain A: A.295, D.296, N.297 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: 4 residues within 4Å: Chain A: Q.235, N.236 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.3: 6 residues within 4Å: Chain A: D.214, N.230, T.232, S.233 Ligands: NAG-NAG-FUC.2, NAG-NAG-FUC.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.232 Water bridges: A:T.232

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

NAG.4: 3 residues within 4Å: Chain A: F.61, N.63, S.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.65 NAG.5: 9 residues within 4Å: Chain A: W.401, C.403, T.406, V.408, N.410, T.412, S.418, V.421, K.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.412, A:S.418

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: L.521, D.561, I.562 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.562 CA.7: 6 residues within 4Å: Chain A: D.389, L.390, I.433, V.434, L.478 Ligands: EDO.12 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain A: T.168, L.209, I.250 No protein-ligand interaction detected (PLIP)

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: E.404, R.431, L.447 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.404, A:R.431 EDO.10: 4 residues within 4Å: Chain A: G.74, R.99, D.327, I.329 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.316 EDO.11: 4 residues within 4Å: Chain A: D.342, Y.343, P.345, H.563 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.392 EDO.12: 8 residues within 4Å: Chain A: V.434, L.478, L.521, T.522, I.562, H.563 Ligands: CA.6, CA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.522, A:H.563 EDO.13: 4 residues within 4Å: Chain A: Q.311, K.312, S.313, Q.558 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.312, A:S.313, A:Q.558 EDO.14: 5 residues within 4Å: Chain A: N.446, K.453, E.455, R.464, V.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.446, A:K.453, A:E.455, A:R.464 EDO.15: 4 residues within 4Å: Chain A: Q.311, R.555, I.556, A.557 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.311, A:A.557

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
E3.18 Disulfide constrained peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low-density lipoprotein receptor-related protein 6

E3.18 Disulfide constrained peptide

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