SMTL ID : 4n4w.1

Structure of the human smoothened receptor in complex with SANT-1.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 2 residues within 4Å: Chain A: D.129, A.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.129 NAG-NAG-BMA-MAN.9: 2 residues within 4Å: Chain B: D.129, A.412 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.129, B:D.129

2 x SNT: (E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methanimine(Non-covalent)

SNT.2: 21 residues within 4Å: Chain A: M.150, F.194, W.201, L.245, M.246, V.249, D.304, V.306, S.307, I.309, F.311, Y.314, I.328, V.383, T.386, H.390, E.438, N.441, L.442, M.445, T.448 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.194, A:F.194, A:W.201, A:L.245, A:V.249, A:V.306, A:I.309, A:F.311, A:V.383, A:T.386, A:E.438, A:E.438, A:N.441, A:L.442, A:L.442 pi-Stacking: A:W.201 SNT.10: 21 residues within 4Å: Chain B: M.150, F.194, W.201, L.245, M.246, V.249, D.304, V.306, S.307, I.309, F.311, Y.314, I.328, V.383, T.386, H.390, E.438, N.441, L.442, M.445, T.448 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.194, B:F.194, B:W.201, B:L.245, B:V.249, B:V.306, B:I.309, B:F.311, B:V.383, B:T.386, B:E.438, B:E.438, B:N.441, B:L.442, B:L.442 Hydrogen bonds: B:Y.314 pi-Stacking: B:W.201

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.66, D.69 Chain B: H.66, D.69 Ligands: ZN.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.66, B:D.69, A:H.66, A:D.69 ZN.4: 2 residues within 4Å: Chain A: N.352, H.353 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.353, H2O.1 ZN.11: 5 residues within 4Å: Chain A: H.66, D.69 Chain B: H.66, D.69 Ligands: ZN.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.66, B:D.69, A:H.66, A:D.69 ZN.12: 2 residues within 4Å: Chain B: N.352, H.353 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.353, H2O.1

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

OLC.5: 5 residues within 4Å: Chain A: Y.153, L.436, K.439, I.440, F.443 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.436, A:F.443, A:F.443 Hydrogen bonds: A:Y.153 Water bridges: A:D.149 Salt bridges: A:K.439 OLC.6: 4 residues within 4Å: Chain A: Y.189, Y.243, H.281, W.285 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.243, A:W.285, A:W.285 Hydrogen bonds: A:Y.189 Salt bridges: A:H.281 OLC.13: 5 residues within 4Å: Chain B: Y.153, L.436, K.439, I.440, F.443 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.436, B:F.443, B:F.443 Water bridges: B:K.439 Salt bridges: B:K.439 OLC.14: 4 residues within 4Å: Chain B: Y.189, Y.243, H.281, W.285 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.243, B:W.285, B:W.285 Salt bridges: B:H.281

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 2 residues within 4Å: Chain A: I.105, R.119 No protein-ligand interaction detected (PLIP) PEG.15: 2 residues within 4Å: Chain B: I.105, R.119 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 5 residues within 4Å: Chain A: R.371, W.457, T.458, K.459, L.462 No protein-ligand interaction detected (PLIP) PG4.16: 5 residues within 4Å: Chain B: R.371, W.457, T.458, K.459, L.462 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Structural basis for Smoothened receptor modulation and chemoresistance to anticancer drugs. Nat Commun (2014)

Release Date

2014-01-22

Peptides

Cytochrome b(562),Smoothened homolog: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b(562),Smoothened homolog

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