SMTL ID : 7drt.1

Human Wntless in complex with Wnt3a

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(Non-covalent)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.87, F.290, G.291, D.294, R.295 No protein-ligand interaction detected (PLIP)

1 x PAM: PALMITOLEIC ACID(Covalent)

PAM.2: 11 residues within 4Å: Chain A: L.208, S.209 Chain B: I.302, G.305, I.306, A.343, S.346, F.347, L.349, F.350, D.353 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.302, B:I.306, B:F.347, B:L.349, B:F.350, A:L.208

2 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.3: 11 residues within 4Å: Chain A: G.144, S.145, P.146, W.152 Chain B: F.24, V.31, K.232, V.233, A.236, T.239, F.240 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.31, B:A.236, B:T.239, B:F.240, B:F.240, B:F.240 PCW.6: 15 residues within 4Å: Chain A: V.214 Chain B: Q.226, F.230, W.234, M.277, I.280, R.303, F.307, Y.308, A.443, T.446, V.447, F.474, Y.478, W.481 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.307, B:F.307, B:Y.308, B:A.443, B:T.446, B:V.447, B:W.481, B:W.481 Hydrogen bonds: B:R.303 pi-Cation interactions: B:W.234, B:F.474

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 5 residues within 4Å: Chain B: T.239, P.243, P.283, W.286, F.287 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.239, B:P.243, B:P.283, B:W.286, B:W.286, B:F.287, B:F.287

1 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.5: 8 residues within 4Å: Chain B: T.257, M.259, R.261, P.262, P.263, A.272, I.275, S.276 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.272, B:I.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, Q. et al., Cryo-EM structure of human Wntless in complex with Wnt3a. Nat Commun (2021)

Release Date

2021-07-14

Peptides

Protein Wnt-3a: A
Protein wntless homolog: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Protein Wnt-3a

Protein wntless homolog

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