SMTL ID : 4a0p.1

Crystal structure of LRP6P3E3P4E4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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.1: 4 residues within 4Å: Chain A: D.48, F.65, N.67, S.69 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.48 Water bridges: A:R.50, A:R.50 NAG-NAG.2: 6 residues within 4Å: Chain A: W.405, N.414, T.416, G.420, S.422, V.425 No protein-ligand interaction detected (PLIP)

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

NAG.3: 6 residues within 4Å: Chain A: D.218, Y.219, N.234, T.236, S.237, N.240 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.218 Hydrogen bonds: A:D.218, A:D.218, A:N.234, A:T.236 NAG.4: 2 residues within 4Å: Chain A: A.299, N.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.299, A:N.301

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

CA.5: 1 residues within 4Å: Chain A: D.253 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.253, H2O.1, H2O.2, H2O.2, H2O.17 CA.6: 3 residues within 4Å: Chain A: L.185, N.188, P.208 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.185, A:P.208, H2O.5, H2O.5, H2O.6 CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain A: V.438, A.483, L.484 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: F.472, F.473, S.474, R.511 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: P.163, N.164, R.200 Ligand excluded by PLIP

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

EDO.10: 9 residues within 4Å: Chain A: K.443, G.444, Y.445, A.462, E.467, L.594, V.595, K.596, G.597 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.444, A:G.597 Water bridges: A:Y.445, A:Y.445, A:D.598, A:D.598 EDO.11: 3 residues within 4Å: Chain A: V.118, W.119, K.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.119, A:K.120, A:K.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Structural and Functional Studies of Lrp6 Ectodomain Reveal a Platform for Wnt Signaling. Dev.Cell (2011)

Release Date

2011-10-26

Peptides

LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6