SMTL ID : 5gje.1

Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

4 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: N.262, A.263, T.264 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: V.464, N.467 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: R.412, N.414, T.416, M.417 Ligands: PO4.7 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: I.384, W.400, N.409, T.411, G.415, S.417, V.420 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.417

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.4: 5 residues within 4Å: Chain B: D.43, N.44, F.60, N.62, S.64 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 6 residues within 4Å: Chain A: T.169, L.211, T.212, H.253, A.254, R.259 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.169, A:L.211, A:T.212, A:A.254 Salt bridges: A:H.253, A:R.259 PO4.7: 3 residues within 4Å: Chain A: R.396, L.413 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.396

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

NAG.8: 6 residues within 4Å: Chain B: D.213, Y.214, N.229, T.231, S.232 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.231 NAG.9: 2 residues within 4Å: Chain B: N.235 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain B: A.294, N.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.294

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 1 residues within 4Å: Chain B: R.355 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.355, B:R.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matoba, K. et al., Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1. Cell Rep (2017)

Release Date

2017-01-18

Peptides

Low-density lipoprotein receptor-related protein 6: A
Low-density lipoprotein receptor-related protein 6: B
Dickkopf-related protein 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Low-density lipoprotein receptor-related protein 6

Low-density lipoprotein receptor-related protein 6

Dickkopf-related protein 1

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