SMTL ID : 6rmg.1

Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-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: 8 residues within 4Å: Chain A: L.818, D.821, R.824, S.825, I.997, N.1000, Y.1001, L.1004 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: A.306, K.311, N.312 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.306, A:K.311 Hydrogen bonds: A:N.312, A:N.312 NAG.3: 9 residues within 4Å: Chain A: D.318, A.320, L.321, N.349, S.350, T.351, K.353, L.354, V.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.349 NAG.4: 3 residues within 4Å: Chain A: A.412, N.414, S.415 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: I.868, N.872, N.875 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.875, A:N.875 NAG.6: 2 residues within 4Å: Chain A: N.141, Q.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.141

11 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 10 residues within 4Å: Chain A: A.113, V.114, L.116, K.117, L.475, A.478, L.479, A.482 Ligands: Y01.8, Y01.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.116, A:K.117, A:L.475, A:L.479 Salt bridges: A:K.117 Y01.8: 11 residues within 4Å: Chain A: V.437, V.439, V.442, A.443, Y.446, L.447, L.450, L.475, A.478 Ligands: Y01.7, Y01.9 No protein-ligand interaction detected (PLIP) Y01.9: 15 residues within 4Å: Chain A: L.116, A.119, L.121, V.437, V.442, Y.446, A.478, V.481, A.482, L.485, F.495, T.500, P.504 Ligands: Y01.7, Y01.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.116, A:A.119, A:L.121, A:V.442, A:Y.446, A:L.485, A:F.495 Y01.10: 8 residues within 4Å: Chain A: I.1074, L.1134, R.1150, F.1153, A.1154, A.1157, I.1158, I.1161 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1150 Y01.11: 8 residues within 4Å: Chain A: F.755, L.758, G.759, G.762, V.763, Y.766, R.770 Ligands: Y01.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.763, A:Y.766 Hydrogen bonds: A:Y.766 Salt bridges: A:R.770 Y01.12: 8 residues within 4Å: Chain A: L.758, L.761, G.762, L.765, Y.766, T.769 Ligands: Y01.11, Y01.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.765 Y01.13: 12 residues within 4Å: Chain A: L.765, T.768, T.769, R.1025, L.1028, L.1029, I.1032, T.1064, V.1065, F.1068, L.1086 Ligands: Y01.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1028, A:F.1068 Y01.14: 12 residues within 4Å: Chain A: Y.93, N.97, K.100, F.101, V.104, G.105, I.108, F.109, F.112, F.583, A.586, L.590 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.93, A:F.101, A:F.101, A:V.104, A:F.109, A:F.583, A:A.586 Hydrogen bonds: A:Y.93 Y01.15: 8 residues within 4Å: Chain A: A.468, I.595, M.598, D.599, Y.601, R.602, R.607, F.611 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.601, A:Y.601, A:F.611 Y01.16: 6 residues within 4Å: Chain A: L.62, S.66, K.74, A.75, W.78, L.79 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.74, A:A.75, A:W.78, A:W.78 Y01.17: 29 residues within 4Å: Chain A: S.206, L.209, M.216, I.219, I.220, L.223, Y.224, P.225, L.227, W.256, F.259, P.261, F.264, L.265, W.278, M.281, L.282, A.285, V.287, L.330, S.331, Y.334, M.335, W.337, V.932, A.935, A.936, Q.938, Y.977 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.209, A:I.219, A:I.219, A:I.220, A:Y.224, A:P.225, A:W.256, A:F.264, A:L.265, A:L.282, A:V.932 Hydrogen bonds: A:S.206

1 x ZN: ZINC ION(Non-covalent)

ZN.18: 6 residues within 4Å: Chain B: H.222, H.228, D.235, E.264, H.268, H.270 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.228, B:D.235, B:D.235, B:H.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qi, C. et al., Structural basis of sterol recognition by human hedgehog receptor PTCH1. Sci Adv (2019)

Release Date

2019-10-09

Peptides

Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related: A
Sonic hedgehog protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related

Sonic hedgehog protein