SMTL ID : 6rvd.1

Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

1 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.821, N.1000, L.1004 No protein-ligand interaction detected (PLIP)

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

CLR.2: 5 residues within 4Å: Chain A: A.119, L.121, V.437, F.495, P.504 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.121, A:V.437, A:F.495, A:F.495, A:P.504 CLR.8: 17 residues within 4Å: Chain B: S.206, L.209, M.216, I.219, I.220, Y.224, P.225, P.261, W.278, M.281, L.282, A.285, S.331, Y.334, M.335, V.932, A.936 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.209, B:I.219, B:I.220, B:Y.224, B:P.261, B:W.278, B:Y.334, B:Y.334, B:V.932, B:A.936 CLR.9: 7 residues within 4Å: Chain B: L.116, A.119, L.121, V.437, Y.446, F.495, P.504 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.116, B:A.119, B:F.495, B:F.495, B:P.504 CLR.13: 18 residues within 4Å: Chain A: M.216, I.219, I.220, L.223, Y.224, P.225, L.248, W.256, F.259, P.261, F.264, L.265, W.278, V.287, L.330, S.331, M.335 Chain C: G.174 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.219, A:I.220, A:Y.224, A:P.225, A:L.248, A:W.256, A:F.259, A:P.261, A:F.264, A:L.265, A:W.278, A:W.278, A:W.278, A:V.287, A:L.330

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

NAG.3: 3 residues within 4Å: Chain A: A.306, K.311, N.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.312 NAG.4: 2 residues within 4Å: Chain A: N.349, T.351 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.351 NAG.5: 1 residues within 4Å: Chain A: N.414 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.871, N.872, N.875 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.872, A:N.875 NAG.7: 3 residues within 4Å: Chain A: R.138, N.141, Q.145 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.138 Hydrogen bonds: A:Q.145 NAG.10: 2 residues within 4Å: Chain B: A.412, N.414 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.412 NAG.11: 2 residues within 4Å: Chain B: N.1000, L.1004 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1000

1 x PLM: PALMITIC ACID(Covalent)

PLM.12: 15 residues within 4Å: Chain A: L.128, W.129, L.427, L.431, F.434, N.496, A.498, A.569, L.570, L.777, I.780, F.1017, V.1081 Chain C: C.1, G.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.128, A:W.129, A:L.427, A:L.431, A:F.434, A:A.498, A:A.569, A:L.570, A:L.777, A:L.777, A:I.780, A:F.1017, A:V.1081 Hydrogen bonds: C:G.2

1 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain C: H.117, D.124, E.153, H.159 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.117, C:D.124, C:D.124, C:E.153, C:H.159

2 x CA: CALCIUM ION(Non-covalent)

CA.15: 4 residues within 4Å: Chain C: E.67, E.103, D.106, D.108 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.67, C:E.103, C:E.103, C:D.106, C:D.108 CA.16: 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.67, C:D.72, C:T.102, C:E.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolf, A.F. et al., The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism. Nat.Chem.Biol. (2019)

Release Date

2019-10-02

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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