SMTL ID : 6h15.1

Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-mer

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: 3 residues within 4Å: Chain A: F.61, N.63, S.65 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain D: N.45, F.61, N.63, S.65 No protein-ligand interaction detected (PLIP)

2 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.2: 7 residues within 4Å: Chain A: V.374, W.401, N.410, T.412, G.416, S.418, V.421 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.418 NAG-NAG-BMA.5: 6 residues within 4Å: Chain D: W.401, N.410, T.412, G.416, S.418, V.421 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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: 4 residues within 4Å: Chain D: D.214, N.230, T.232, S.233 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: D.214, Y.215, N.230, S.233 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.214 Hydrogen bonds: A:N.230 NAG.7: 2 residues within 4Å: Chain A: Q.235, N.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.236 NAG.8: 2 residues within 4Å: Chain A: A.295, N.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.295 NAG.13: 2 residues within 4Å: Chain D: Q.235, N.236 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain D: A.295, D.296, N.297 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.295, D:N.297

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

CL.9: 2 residues within 4Å: Chain A: I.508, V.509 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: Q.553, A.554 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: Q.56, T.57 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: S.70, R.71 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain D: L.29, T.30, G.31, V.32 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: A.129, G.260, W.261 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain D: R.99, E.101, R.110, I.328, I.329 Ligand excluded by 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: AD
VHH L-P2-B10: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
C

C
D

Low-density lipoprotein receptor-related protein 6

VHH L-P2-B10