SMTL ID : 6n7k.1

Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form II)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

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

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

NAG.5: 2 residues within 4Å: Chain A: A.327, N.333 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.370, K.374, L.375, V.376 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.435 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.893, N.896 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.162 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.162, Q.166 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: A.327, N.333 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.370 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: A.433, N.435 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: K.888, N.896 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: A.327, N.333 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.370, K.374, L.375, V.376 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.435 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.893, N.896 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.162 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: N.162, Q.166 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: A.327, N.333 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.370 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: A.433, N.435 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: K.888, N.896 Ligand excluded by PLIP

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

CLR.10: 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.11: 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.12: 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.18: 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.19: 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 CLR.29: 10 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:L.230, D:I.241, D:Y.245, D:W.277, D:F.280, D:L.303, D:V.953 CLR.30: 12 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:L.149, D:W.150, D:W.150, D:F.455, D:F.455, D:A.519, D:L.798, D:L.798, D:I.801, D:I.801, D:F.1038, D:F.1038, D:F.1038, D:F.1168, D:F.1168, D:F.1173 CLR.31: 9 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:L.142, D:V.458, D:Y.467, D:V.502, D:A.503, D:L.506, D:F.516 CLR.37: 7 residues within 4Å: Chain E: A.140, L.142, V.458, V.463, L.506, T.521, P.525 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.140, E:L.142, E:V.458, E:V.463, E:L.506, E:T.521, E:P.525 CLR.38: 10 residues within 4Å: Chain E: M.237, I.240, I.241, L.244, F.285, W.299, L.303, V.308, L.351 Chain F: G.174 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.240, E:I.241, E:F.285, E:W.299, E:W.299, E:L.303, E:V.308, E:L.351

2 x ZN: ZINC ION(Non-covalent)

ZN.20: 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 ZN.39: 4 residues within 4Å: Chain F: H.117, D.124, E.153, H.159 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.117, F:D.124, F:D.124, F:H.159

4 x CA: CALCIUM ION(Non-covalent)

CA.21: 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.22: 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 CA.40: 3 residues within 4Å: Chain F: E.66, E.67, D.106 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.67 CA.41: 5 residues within 4Å: Chain F: E.66, E.67, D.72, T.102, E.103 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.66, F:E.66, F:D.72, F:D.72, F:T.102

2 x PLM: PALMITIC ACID(Covalent)

PLM.23: 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 PLM.42: 10 residues within 4Å: Chain E: L.149, W.150, F.455, L.796, L.798, I.801, Y.822, F.1038, F.1168 Chain F: C.1 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.149, E:W.150, E:F.455, E:L.796, E:I.801, E:I.801, E:F.1038, E:F.1168, E: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: ABDE
Sonic hedgehog protein: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

E
E

C
C

F
F

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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