SMTL ID : 7kc4.1

Human WLS in complex with WNT8A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 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: 2 residues within 4Å: Chain A: N.262, L.265 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.2: 9 residues within 4Å: Chain A: S.42, L.45, I.99, N.103, M.106, D.108, F.109 Chain B: R.75, E.79 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.75

1 x PLM: PALMITIC ACID(Covalent)

PLM.3: 14 residues within 4Å: Chain A: I.185, S.186 Chain B: D.301, G.305, I.306, A.309, M.310, S.313, Q.338, S.346, L.349, F.350, D.353 Ligands: DR9.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.306, B:A.309, B:L.349, B:F.350, A:I.185

3 x DR9: 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL(Non-covalent)

DR9.4: 23 residues within 4Å: Chain A: K.181, C.182, I.185, S.186, G.187, S.188 Chain B: G.305, Y.308, L.312, P.341, I.342, G.345, S.346, L.349, F.352, W.369, M.379, I.382, I.383, G.386, C.388, C.390 Ligands: PLM.3 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.308, B:Y.308, B:L.312, B:L.349, B:F.352, B:I.383, A:I.185 Hydrogen bonds: A:C.182, A:G.187 DR9.5: 23 residues within 4Å: Chain A: S.190 Chain B: Q.226, W.234, K.238, M.277, G.300, Q.304, F.307, Y.308, W.315, F.393, L.396, M.436, T.439, L.440, A.443, T.446, F.450, I.451, F.473, F.474, Y.478, W.481 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.307, B:Y.308, B:W.315, B:F.393, B:L.396, B:T.439, B:L.440, B:A.443, B:T.446, B:F.450, B:I.451, B:F.473, B:F.474, B:F.474, B:W.481 Hydrogen bonds: B:Q.226, B:Y.308 Salt bridges: B:K.238 DR9.6: 17 residues within 4Å: Chain B: M.9, T.11, C.15, G.18, L.21, L.22, Q.25, F.430, F.434, L.437, I.438, A.441, C.442, M.480, L.483, Y.484, A.487 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.21, B:L.21, B:Q.25, B:F.434, B:F.434, B:L.437, B:I.438, B:I.438, B:I.438, B:A.441 Hydrogen bonds: B:M.9

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 9 residues within 4Å: Chain B: F.246, M.249, V.250, R.254, T.257, M.258, T.278, F.279, I.282 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.246, B:V.250, B:R.254, B:T.278, B:F.279, B:I.282 Hydrogen bonds: B:R.254 Salt bridges: B:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nygaard, R. et al., Structural Basis of WLS/Evi-Mediated Wnt Transport and Secretion. Cell (2021)

Release Date

2021-01-06

Peptides

Protein Wnt-8a: A
Protein wntless homolog: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

Membrane

We predict this structure to be a membrane protein.
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Protein Wnt-8a

Protein wntless homolog