SMTL ID : 8dvm.1

Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- NAG- FUC- FUC- FUC- FUC: alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-FUC-FUC-FUC-FUC.1: 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:N.45 Water bridges: A:D.44

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

NAG-NAG.2: 7 residues within 4Å: Chain A: D.214, Y.215, N.230, T.232, S.233, N.236 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: A.295, N.297 No protein-ligand interaction detected (PLIP)

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.4: 8 residues within 4Å: Chain A: L.383, W.401, N.410, T.412, G.416, S.418, V.421 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.418

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

NAG.5: 3 residues within 4Å: Chain A: Y.215, N.236 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.236

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.6: 1 residues within 4Å: Ligands: CA.8 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain A: T.95, N.98, S.120 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.95, A:S.120, H2O.2, H2O.5, H2O.9 CA.8: 5 residues within 4Å: Chain A: L.521, T.522, D.561, I.562 Ligands: CA.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.521, A:I.562, H2O.1, H2O.4, H2O.5

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

EDO.9: 5 residues within 4Å: Chain A: W.138, R.163 Chain B: W.4, W.8, F.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 EDO.10: 2 residues within 4Å: Chain A: R.223, I.239 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: F.309, D.327, Q.553, I.556 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.327, A:Q.553 EDO.12: 5 residues within 4Å: Chain A: K.312, N.337, V.338, K.533 Ligands: MES.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.337 Water bridges: A:S.355, A:S.355 EDO.13: 5 residues within 4Å: Chain A: K.88, K.104, L.105, D.106, Q.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.104, A:L.105, A:Q.108 EDO.14: 5 residues within 4Å: Chain A: L.113, V.114, W.115, K.116, G.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.115, A:K.116, A:K.116, A:G.151 EDO.15: 5 residues within 4Å: Chain A: D.342, Y.343, I.392, I.394, H.563 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.392 Water bridges: A:I.392 EDO.16: 5 residues within 4Å: Chain A: S.418, G.420, V.421, H.604 Ligands: NAG-NAG-BMA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.418, A:S.418, A:V.421 EDO.17: 7 residues within 4Å: Chain A: T.304, Y.343, P.345, K.348, V.565, E.567, L.568 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.343, A:K.348, A:L.568 EDO.18: 4 residues within 4Å: Chain A: G.485, D.501, L.502, S.503 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.502, A:S.503, A:S.503 EDO.19: 7 residues within 4Å: Chain A: K.439, G.440, Y.441, A.458, E.463, V.591, K.592 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.441, A:R.598 EDO.20: 6 residues within 4Å: Chain A: A.172, Q.211, Y.212, Q.213, S.256, R.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.211, A:Q.213 Water bridges: A:D.170, A:Y.171 EDO.21: 5 residues within 4Å: Chain A: E.404, A.405, N.407, R.429, R.431 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.407, A:R.431 EDO.22: 3 residues within 4Å: Chain A: Q.108, H.109, P.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.109, A:H.109 Water bridges: A:G.107, A:R.110, A:H.273

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.23: 9 residues within 4Å: Chain A: R.339, Y.388, D.389, I.476, V.519, K.533, S.560, D.561 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.533

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
E3.6 Disulfide constrained peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low-density lipoprotein receptor-related protein 6

E3.6 Disulfide constrained peptide

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