SMTL ID : 7k65.1

Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23

Coordinates

PDB Format Compare

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: 3 residues within 4Å: Chain A: D.783, N.962, Y.963 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.783

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

NAG.2: 1 residues within 4Å: Chain A: N.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.400 NAG.3: 2 residues within 4Å: Chain A: N.127, Q.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.131 NAG.4: 2 residues within 4Å: Chain A: K.297, N.298 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: R.829, K.836, N.837 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.829 NAG.6: 3 residues within 4Å: Chain A: N.335, T.337, G.338 No protein-ligand interaction detected (PLIP)

4 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)

Q7G.7: 30 residues within 4Å: Chain A: V.111, L.114, W.115, N.140, L.143, L.327, Q.347, M.349, F.408, T.410, L.413, L.417, F.420, A.483, A.484, L.556, L.737, L.739, I.742, Q.756, F.760, F.762, Y.763, N.764, Y.975, F.979, W.980, V.1043, F.1109, F.1114 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.111, A:L.114, A:W.115, A:W.115, A:L.417, A:F.420, A:A.483, A:A.484, A:L.556, A:L.739, A:I.742, A:I.742, A:F.979 Hydrogen bonds: A:T.410, A:Q.756, A:Q.756, A:F.760, A:Y.975 Q7G.8: 10 residues within 4Å: Chain A: L.102, A.105, L.107, V.423, V.428, Y.432, L.471, F.481, T.485, P.490 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.102, A:A.105, A:L.107, A:L.107, A:V.423, A:Y.432, A:L.471, A:F.481, A:P.490 Q7G.9: 9 residues within 4Å: Chain A: I.206, Y.210, W.242, F.245, L.251, L.254, W.264, L.268 Chain B: F.29 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.206, A:Y.210, A:W.242, A:F.245, A:L.251, A:L.254, A:W.264, A:W.264, A:W.264, A:W.264, A:L.268, B:F.29 Q7G.10: 5 residues within 4Å: Chain A: R.1112, A.1116, A.1119, I.1120, V.1123 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1116, A:A.1119, A:I.1120, A:V.1123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2021-03-17

Peptides

Protein patched homolog 1: A
nanobody TI23: 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

nanobody TI23