SMTL ID : 8ffe.1

Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 3 residues within 4Å: Chain A: V.464, N.467, T.468 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.464

1 x NAG- NAG- BMA- FUC- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC-FUC.2: 6 residues within 4Å: Chain A: R.412, N.414, T.416, M.417, S.581, H.582 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.412 Water bridges: A:R.412, A:S.581

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

NAG-MAN-NAG.3: 3 residues within 4Å: Chain A: N.262, A.263, T.264 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.264

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: T.293, G.294, A.308, L.311, R.322, S.324, I.333, I.370 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.293, A:A.308, A:R.322, A:R.322 Water bridges: A:S.324 GOL.5: 8 residues within 4Å: Chain A: D.347, I.389, A.390, I.432, V.433, L.434, Y.480, K.560 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.389, A:L.434, A:L.434 Water bridges: A:V.391, A:I.432, A:I.432, A:L.478, A:T.520, A:K.560 GOL.6: 5 residues within 4Å: Chain A: E.88, K.89, N.104, L.105, D.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.88, A:L.105, A:D.106, A:D.106 GOL.7: 6 residues within 4Å: Chain A: G.74, L.76, T.97, R.99, R.321, V.334 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.74, A:R.99, A:R.321, A:R.321 Water bridges: A:G.74, A:G.74 GOL.11: 2 residues within 4Å: Chain A: K.494, E.510 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.494 Water bridges: A:K.494 GOL.12: 5 residues within 4Å: Chain B: V.126, Q.151, G.152, T.153, L.154 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.154 Water bridges: B:Q.151, C:G.44 GOL.13: 5 residues within 4Å: Chain C: Q.40, K.48, V.61, P.62, F.65 4 PLIP interactions: 4 interactions with chain C Water bridges: C:Q.40, C:L.49, C:G.60, C:R.64

3 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: S.95, N.98, D.119, Q.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.98, A:D.119 Water bridges: A:Q.120 NA.9: 3 residues within 4Å: Chain A: T.403, D.406, E.427 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.403, A:T.403 NA.10: 3 residues within 4Å: Chain A: A.490, D.493, P.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.490

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.14: 5 residues within 4Å: Chain B: S.133, G.134, Y.142 Chain C: Y.52, Y.58 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.52 Hydrogen bonds: C:Y.52, B:S.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutsumi, N. et al., Structure of the Wnt-Frizzled-LRP6 initiation complex reveals the basis for coreceptor discrimination. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-03-08

Peptides

Low-density lipoprotein receptor-related protein 6: A
YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker: B
YW210.09 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Low-density lipoprotein receptor-related protein 6

YW210.09 Fab heavy chain with engineered XWnt8 NC peptide and linker

YW210.09 Fab light chain