SMTL ID : 7urd.1

Human PORCN in complex with LGK974 and WNT3A peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x O50: 2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide(Non-covalent)

O50.1: 18 residues within 4Å: Chain A: V.305, W.308, S.313, L.316, N.317, F.321, T.336, Y.337, S.340, H.344, L.350, V.353, L.354, L.357, L.413, L.416, G.417, F.420 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.305, A:T.336, A:L.350, A:L.357, A:L.416, A:F.420 Hydrogen bonds: A:V.305, A:S.340 pi-Stacking: A:W.308, A:W.308

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 5 residues within 4Å: Chain A: V.439, W.447, H.450, W.451, F.454 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.447, A:W.447, A:W.447, A:H.450, A:W.451, A:F.454 CLR.3: 5 residues within 4Å: Chain A: R.14, Q.15, F.18, F.226, I.227 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.18, A:F.18, A:F.226, A:I.227 Hydrogen bonds: A:Q.15

1 x AJP: Digitonin(Non-covalent)

AJP.4: 16 residues within 4Å: Chain A: V.105, S.108, V.143, F.147, W.315, Y.319, V.320, N.323, A.324, R.326, V.335, L.342 Chain D: Y.73, Y.74, V.75, R.93 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:V.143, A:F.147, A:F.147, A:A.324, A:L.342 Hydrogen bonds: A:R.326, D:R.93, D:R.93 Salt bridges: A:R.326, A:R.326, A:R.326, D:R.93

1 x OLA: OLEIC ACID(Non-covalent)

OLA.5: 10 residues within 4Å: Chain A: A.352, L.355, S.356, F.359, Y.362, V.363, W.442, T.453, F.454, W.457 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.352, A:L.355, A:F.359, A:F.359, A:Y.362, A:V.363, A:W.442 Hydrogen bonds: A:Y.362

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.378, C.384, C.388, H.390 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.378, A:C.384, A:C.388, A:H.390

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Mechanisms and inhibition of Porcupine-mediated Wnt acylation. Nature (2022)

Release Date

2022-07-20

Peptides

Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine: A
Isoform 2 of Protein Wnt-3a peptide: B
2C11 light chain: C
2C11 heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
L

D
H

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine

Isoform 2 of Protein Wnt-3a peptide

2C11 light chain

2C11 heavy chain

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