SMTL ID : 7v6y.1

Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.5 angstrom (re-processed with dataset of 7dzq)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.893, Y.894, L.897 No protein-ligand interaction detected (PLIP)

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 16 residues within 4Å: Chain A: K.193, S.194, G.195, L.197, I.207, L.211, P.213, W.244, F.247, F.252, L.270, A.273, V.275, M.323, V.825, A.828 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.197, A:I.207, A:P.213, A:W.244, A:F.247, A:F.252, A:A.273, A:V.275, A:V.825 CLR.3: 11 residues within 4Å: Chain A: L.104, A.107, L.109, V.425, A.431, Y.434, A.466, V.469, L.473, T.488, P.492 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.425, A:Y.434, A:V.469, A:L.473, A:P.492

1 x 5VI: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid(Non-covalent)

5VI.4: 13 residues within 4Å: Chain A: V.113, E.114, M.351, F.410, L.415, L.670, Q.687, F.688, F.693, Y.694, Y.906, F.910, W.911 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.670, A:F.688, A:F.688, A:F.693, A:Y.694, A:Y.694, A:Y.906, A:Y.906, A:W.911 Hydrogen bonds: A:E.114, A:E.114, A:Y.906

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

NAG.5: 1 residues within 4Å: Chain A: N.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 NAG.6: 3 residues within 4Å: Chain A: N.337, T.339, K.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.337, A:T.339 NAG.7: 1 residues within 4Å: Chain A: N.402 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Y. et al., Cryo-EM study of patched in lipid nanodisc suggests a structural basis for its clustering in caveolae. Structure (2021)

Release Date

2021-09-22

Peptides

Protein patched homolog 1,Protein patched homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Protein patched homolog 1,Protein patched homolog 1