SMTL ID : 3s2k.1

Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-1-mer

Ligands

2 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(Post Translational Modification)

NAG-NAG-FUC.1: 4 residues within 4Å: Chain A: N.47, F.63, N.65, S.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.47, A:N.65 NAG-NAG-FUC.3: 5 residues within 4Å: Chain B: D.46, N.47, F.63, N.65, S.67 No protein-ligand interaction detected (PLIP)

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: I.387, W.403, N.412, T.414, G.418, S.420, V.423 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: I.387, W.403, N.412, T.414, G.418, S.420, V.423 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.420

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

NAG.5: 5 residues within 4Å: Chain A: N.232, T.234, S.235, N.238 Ligands: NAG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.232, A:T.234, A:S.235 NAG.6: 2 residues within 4Å: Chain A: N.238 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: A.297, N.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.297, A:N.299 NAG.9: 6 residues within 4Å: Chain B: D.216, Y.217, N.232, T.234, S.235 Ligands: NAG.10 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain B: N.238 Ligands: NAG.9 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: A.297, N.299 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.297

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: I.343, D.344, L.392, S.393, I.435, V.436, L.523, D.563, I.564, H.565 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.435, A:T.524, A:T.524, A:D.563 GOL.12: 1 residues within 4Å: Chain B: R.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.358, B:R.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahn, V.E. et al., Structural Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6. Dev.Cell (2011)

Release Date

2011-11-02

Peptides

Low-density lipoprotein receptor-related protein 6: AB
Dickkopf-related protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Low-density lipoprotein receptor-related protein 6

Dickkopf-related protein 1