SMTL ID : 6o3c.1

Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: H.303, K.307, R.384 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.303, A:K.307, A:R.384

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

NA.2: 4 residues within 4Å: Chain A: T.53, A.56, S.59, D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.53, A:D.60

6 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.3: 6 residues within 4Å: Chain A: N.359, R.361, Y.362, G.365, F.366 Ligands: OLB.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.361, A:F.366 Hydrogen bonds: A:N.359 OLB.4: 5 residues within 4Å: Chain A: L.375, G.379, Y.380, I.383, M.387 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.380 OLB.5: 10 residues within 4Å: Chain A: Y.360, R.361, A.364, L.368, A.369, G.372, F.430, F.434, F.437 Ligands: OLB.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.369, A:F.430, A:F.430, A:F.430, A:F.434 Hydrogen bonds: A:R.361 OLB.6: 6 residues within 4Å: Chain A: A.364, G.365, A.369, L.373 Ligands: OLB.3, OLB.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.364, A:A.369, A:A.369, A:L.373 OLB.7: 6 residues within 4Å: Chain A: Y.225, Y.232, Y.286, T.320, H.324 Ligands: OLB.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.286 Salt bridges: A:H.324 OLB.8: 9 residues within 4Å: Chain A: V.216, W.219, F.231, A.235, V.239, V.282, I.283, Y.286 Ligands: OLB.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.219, A:F.231, A:A.235, A:V.239, A:V.239, A:V.282, A:Y.286, A:Y.286

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

NAG.9: 2 residues within 4Å: Chain A: R.37, N.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.39 NAG.10: 4 residues within 4Å: Chain A: L.71, R.124, N.456 Ligands: CLR.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.71 Hydrogen bonds: A:R.124

1 x LKD: 3-chloro-4,7-difluoro-N-{[2-methoxy-5-(pyridin-4-yl)phenyl]methyl}-N-[trans-4-(methylamino)cyclohexyl]-1-benzothiophene-2-carboxamide(Non-covalent)

LKD.11: 15 residues within 4Å: Chain A: I.178, N.182, L.184, M.264, G.346, D.347, Y.357, K.358, R.363, D.436, W.443, E.444, F.447, P.476, E.481 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.184, A:Y.357, A:K.358, A:E.444, A:F.447 Hydrogen bonds: A:N.182, A:E.481 pi-Cation interactions: A:K.358

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.12: 16 residues within 4Å: Chain A: L.288, V.292, F.354, Y.357, V.367, I.371, V.374, A.422, V.426, T.429, H.433, N.484, L.485, A.487, M.488, T.491 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.288, A:V.292, A:F.354, A:V.367, A:I.371, A:V.374, A:A.422, A:V.426, A:T.429 Hydrogen bonds: A:Y.357 CLR.13: 10 residues within 4Å: Chain A: D.58, K.68, L.71, W.72, G.74, L.75, I.119, E.123, R.124 Ligands: NAG.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.68, A:L.71, A:L.71, A:L.75, A:I.119, A:E.123, A:R.124 Hydrogen bonds: A:D.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deshpande, I. et al., Smoothened stimulation by membrane sterols drives Hedgehog pathway activity. Nature (2019)

Release Date

2019-07-03

Peptides

Smoothened homolog: A
NbSmo8: 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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Smoothened homolog

NbSmo8