SMTL ID : 3sov.1

The structure of a beta propeller domain in complex with peptide S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

1 x LEU- PRO- ASN- ALA- ILE- GLY- ARG: Sclerostin(Non-covalent)

LEU-PRO-ASN-ALA-ILE-GLY-ARG.1: 15 residues within 4Å: Chain A: R.12, R.13, E.35, D.36, V.54, S.55, D.82, R.125, W.141, W.167, N.169, H.210, F.212, W.226, M.253 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.54, A:D.82, A:W.141, A:W.167, A:W.167, A:F.212, A:W.226 Hydrogen bonds: A:R.12, A:R.12, A:R.13, A:R.13, A:S.55, A:R.125, A:R.125, A:N.169, A:N.169 Salt bridges: A:E.35, A:D.36

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

NAG.2: 6 residues within 4Å: Chain A: F.44, F.64, N.65 Ligands: FUC.3, FUC.4, FUC.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.65, A:N.65 NAG.6: 5 residues within 4Å: Chain A: W.88, L.89, N.265, A.266 Ligands: FUC.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.89 Hydrogen bonds: A:N.265, A:A.266, A:A.266

4 x FUC: alpha-L-fucopyranose(Non-covalent)(Non-functional Binders)

FUC.3: 5 residues within 4Å: Chain A: L.17, F.64, F.258 Ligands: NAG.2, FUC.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.17, A:F.64 FUC.4: 2 residues within 4Å: Ligands: NAG.2, FUC.5 No protein-ligand interaction detected (PLIP) FUC.5: 3 residues within 4Å: Ligands: NAG.2, FUC.3, FUC.4 No protein-ligand interaction detected (PLIP) FUC.7: 6 residues within 4Å: Chain A: A.266, T.267, N.268, G.271, I.272 Ligands: NAG.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.267 Hydrogen bonds: A:N.268, A:N.268 Water bridges: A:L.89, A:E.91

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: W.167, A.185, K.186, N.188, P.209, H.210, S.227 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.186, A:N.188, A:H.210, A:S.227 Water bridges: A:P.209, A:S.227 GOL.9: 5 residues within 4Å: Chain A: E.91, K.92, N.107, L.108, D.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.91, A:L.108, A:D.109, A:D.109 Water bridges: A:E.91, A:K.92 GOL.10: 6 residues within 4Å: Chain A: E.176, L.216, F.217, E.218, Q.261, R.262 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.176, A:E.218, A:Q.261 Water bridges: A:K.236, A:K.236, A:K.236, A:R.262

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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