SMTL ID : 6h16.1

Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-D07

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

3 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.1: 5 residues within 4Å: Chain A: D.44, N.45, F.61, N.63, S.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.44, A:D.44, A:D.44 NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.236 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 1 residues within 4Å: Chain A: N.297 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.4: 8 residues within 4Å: Chain A: V.374, I.385, W.401, N.410, T.412, G.416, S.418, V.421 No protein-ligand interaction detected (PLIP)

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

NAG.5: 5 residues within 4Å: Chain A: Y.215, N.230, S.233, N.236 Ligands: NAG-NAG-BMA.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.215 Hydrogen bonds: A:N.230, A:N.236

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain A: L.478, L.521 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenderico, N. et al., Anti-LRP5/6 VHHs promote differentiation of Wnt-hypersensitive intestinal stem cells. Nat Commun (2019)

Release Date

2019-01-30

Peptides

Low-density lipoprotein receptor-related protein 6: A
VHH L-P2-D07: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Low-density lipoprotein receptor-related protein 6

VHH L-P2-D07