SMTL ID : 6n7h.1

Cryo-EM structure of the 2:1 hPtch1-Shhp complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: D.842, N.1021, Y.1022 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: D.842, N.1021, Y.1022, L.1025 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: A.327, N.333 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.327 NAG.4: 4 residues within 4Å: Chain A: N.370, K.374, L.375, V.376 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.435 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: N.893, N.896 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.893, A:N.896 NAG.7: 1 residues within 4Å: Chain A: N.162 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: N.162, Q.166 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.166 Hydrogen bonds: B:Q.166, B:Q.166 NAG.12: 2 residues within 4Å: Chain B: A.327, N.333 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain B: N.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.371, B:S.371 NAG.14: 2 residues within 4Å: Chain B: A.433, N.435 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.433 NAG.15: 2 residues within 4Å: Chain B: K.888, N.896 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.888, B:K.888, B:N.896

5 x CLR: CHOLESTEROL(Covalent)(Non-covalent)

CLR.8: 10 residues within 4Å: Chain A: L.230, I.241, Y.245, P.246, W.277, F.280, L.303, M.356, V.953, A.957 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.230, A:I.241, A:Y.245, A:W.277, A:F.280, A:L.303, A:V.953 CLR.9: 12 residues within 4Å: Chain A: V.146, L.149, W.150, F.455, A.519, D.797, L.798, I.801, F.1038, W.1039, F.1168, F.1173 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.149, A:W.150, A:W.150, A:F.455, A:F.455, A:A.519, A:L.798, A:L.798, A:I.801, A:I.801, A:F.1038, A:F.1038, A:F.1038, A:F.1168, A:F.1168, A:F.1173 CLR.10: 9 residues within 4Å: Chain A: A.140, L.142, V.458, Y.467, A.499, V.502, A.503, L.506, F.516 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.142, A:V.458, A:Y.467, A:V.502, A:A.503, A:L.506, A:F.516 CLR.16: 7 residues within 4Å: Chain B: A.140, L.142, V.458, V.463, L.506, T.521, P.525 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.140, B:L.142, B:V.458, B:V.463, B:L.506, B:T.521, B:P.525 CLR.17: 10 residues within 4Å: Chain B: M.237, I.240, I.241, L.244, F.285, W.299, L.303, V.308, L.351 Chain C: G.174 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.240, B:I.241, B:F.285, B:W.299, B:W.299, B:L.303, B:V.308, B:L.351

1 x ZN: ZINC ION(Non-covalent)

ZN.18: 4 residues within 4Å: Chain C: H.117, D.124, E.153, H.159 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.117, C:D.124, C:D.124, C:H.159

2 x CA: CALCIUM ION(Non-covalent)

CA.19: 3 residues within 4Å: Chain C: E.66, E.67, D.106 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.67 CA.20: 5 residues within 4Å: Chain C: E.66, E.67, D.72, T.102, E.103 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.66, C:E.66, C:D.72, C:D.72, C:T.102

1 x PLM: PALMITIC ACID(Covalent)

PLM.21: 10 residues within 4Å: Chain B: L.149, W.150, F.455, L.796, L.798, I.801, Y.822, F.1038, F.1168 Chain C: C.1 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.149, B:W.150, B:F.455, B:L.796, B:I.801, B:I.801, B:F.1038, B:F.1168, B:F.1168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, H. et al., Inhibition of tetrameric Patched1 by Sonic Hedgehog through an asymmetric paradigm. Nat Commun (2019)

Release Date

2019-05-29

Peptides

Protein patched homolog 1: AB
Sonic hedgehog protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

Sonic hedgehog protein

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