SMTL ID : 5v57.1

3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 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: 22 residues within 4Å: Chain A: N.162, L.164, F.165, M.173, W.224, D.327, V.329, S.330, I.332, F.334, Y.337, K.338, R.343, H.550, Q.557, W.560, E.561, F.564, P.593, E.598, N.601, L.602 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.224, A:P.593, A:E.598, A:E.598, A:L.602 Hydrogen bonds: A:N.162, A:Y.337, A:R.343, A:R.343 pi-Stacking: A:W.224, A:F.564 836.3: 21 residues within 4Å: Chain B: N.162, L.164, F.165, M.173, W.224, D.327, V.329, S.330, F.334, Y.337, K.338, R.343, H.550, Q.557, W.560, E.561, F.564, P.593, E.598, N.601, L.602 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.224, B:P.593, B:E.598, B:E.598, B:L.602 Hydrogen bonds: B:N.162, B:Y.337, B:R.343, B:R.343 pi-Stacking: B:F.564 Halogen bonds: B:Q.557

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: S.385, T.386, T.387, G.388, N.389, T.390, S.433, T.434, W.435, G.436, C.468, G.469, D.470, W.473, E.474, Y.475, F.476, C.477 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.435, A:W.473 Hydrogen bonds: A:T.386, A:T.387, A:T.387, A:N.389, A:N.389, A:T.390, A:T.390, A:S.433, A:T.434, A:T.434, A:D.470, A:Y.475, A:C.477 pi-Stacking: A:W.473, A:W.473, A:W.473, A:W.473 FMN.4: 18 residues within 4Å: Chain B: S.385, T.386, T.387, G.388, N.389, T.390, S.433, T.434, W.435, G.436, D.437, C.468, G.469, D.470, W.473, Y.475, F.476, C.477 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.435, B:W.435, B:W.473 Hydrogen bonds: B:T.386, B:T.387, B:T.387, B:N.389, B:N.389, B:T.390, B:T.390, B:T.390, B:S.433, B:T.434, B:T.434, B:D.470, B:Y.475, B:C.477 pi-Stacking: B:W.473, B:W.473, B:W.473

1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.5: 9 residues within 4Å: Chain B: W.282, F.286, L.289, I.525, N.526, M.529, L.530, G.533, I.534 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.282, B:I.534 Hydrogen bonds: B:N.526

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