SMTL ID : 3soq.1

The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ACE- ASN- SER- ASN- ALA- ILE- LYS- ASN- NH2: Dickkopf-related protein 1(Non-covalent)

ACE-ASN-SER-ASN-ALA-ILE-LYS-ASN-NH2.1: 15 residues within 4Å: Chain A: R.12, V.54, L.79, S.80, D.82, E.99, R.125, W.141, W.167, N.169, P.209, H.210, W.226, S.227, M.253 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.54, A:D.82, A:W.141, A:W.167 Hydrogen bonds: A:R.12, A:R.12, A:L.79, A:R.125, A:R.125, A:N.169, A:N.169, A:H.210, A:S.227, A:S.227

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 4 residues within 4Å: Chain A: F.44, F.64, N.65 Ligands: FUC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.65

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.3: 4 residues within 4Å: Chain A: L.17, V.30, F.64 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.17, A:V.30, A:F.64

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: E.91, K.92, N.107, L.108, D.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.91, A:L.108, A:D.109, A:D.109

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: S.98, N.101, D.122, Q.123 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.98, A:D.122, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bourhis, E. et al., Wnt antagonists bind through a short peptide to the first beta-propeller domain of LRP5/6. Structure (2011)

Release Date

2011-09-21

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

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