SMTL ID : 5v56.1

2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x 836: N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl)benzamide(Non-covalent)

836.1: 24 residues within 4Å: Chain A: N.167, L.169, F.170, M.178, W.229, M.249, L.251, D.332, V.334, S.335, I.337, F.339, Y.342, K.343, R.348, H.555, Q.562, W.565, E.566, F.569, P.598, E.603, N.606, L.607 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.229, A:V.334, A:P.598, A:E.603, A:E.603, A:L.607 Hydrogen bonds: A:N.167, A:Y.342, A:R.348, A:R.348 pi-Stacking: A:W.229, A:H.555, A:F.569 836.4: 23 residues within 4Å: Chain B: N.167, L.169, F.170, M.178, W.229, M.249, D.332, V.334, S.335, I.337, F.339, Y.342, K.343, R.348, H.555, Q.562, W.565, E.566, F.569, P.598, E.603, N.606, L.607 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.229, B:P.598, B:E.603, B:E.603, B:L.607 Hydrogen bonds: B:N.167, B:Y.342, B:R.348, B:R.348 pi-Stacking: B:F.569 Halogen bonds: B:Q.562

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: S.390, T.391, T.392, G.393, N.394, T.395, S.438, T.439, W.440, G.441, C.473, G.474, D.475, W.478, E.479, Y.480, F.481, C.482 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.440, A:W.478 Hydrogen bonds: A:T.391, A:T.392, A:N.394, A:N.394, A:T.395, A:T.395, A:S.438, A:T.439, A:T.439, A:D.475, A:Y.480, A:C.482 pi-Stacking: A:W.478, A:W.478, A:W.478 FMN.5: 19 residues within 4Å: Chain B: S.390, T.391, T.392, G.393, N.394, T.395, S.438, T.439, W.440, G.441, D.442, C.473, G.474, D.475, W.478, E.479, Y.480, F.481, C.482 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.440, B:W.440, B:W.478 Hydrogen bonds: B:T.391, B:T.392, B:N.394, B:N.394, B:T.395, B:T.395, B:S.438, B:T.439, B:T.439, B:G.474, B:D.475, B:Y.480, B:C.482 pi-Stacking: B:W.478, B:W.478, B:W.478

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

NAG.3: 5 residues within 4Å: Chain A: M.142, N.578, P.588, I.589, P.590 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Nat Commun (2017)

Release Date

2017-05-24

Peptides

Smoothened homolog,Flavodoxin,Smoothened homolog: AB

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,Flavodoxin,Smoothened homolog