SMTL ID : 6dmy.1

Cryo-EM structure of human Ptch1 and ShhN complex

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: 3 residues within 4Å: Chain A: D.842, S.846, N.1021 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.327, K.332, N.333 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.370 NAG.4: 2 residues within 4Å: Chain A: Q.434, N.435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.434 NAG.5: 1 residues within 4Å: Chain A: N.896 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.896 NAG.6: 2 residues within 4Å: Chain A: N.162, Q.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.162

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 21 residues within 4Å: Chain A: S.227, L.230, M.237, I.241, Y.245, P.246, L.248, W.277, F.285, L.286, W.299, M.302, L.303, S.352, Y.355, M.356, W.358, V.953, A.956, A.957, Q.959 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.230, A:I.241, A:Y.245, A:W.277, A:F.285, A:L.286, A:W.299, A:A.956 Hydrogen bonds: A:Q.959 Y01.8: 9 residues within 4Å: Chain A: L.137, A.140, N.141, L.142, V.458, Y.467, A.499, A.503, F.516 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.137, A:A.140, A:V.458, A:V.458, A:Y.467, A:A.499, A:A.503, A:F.516

1 x SER: SERINE(Covalent)

SER.9: 3 residues within 4Å: Chain B: K.166, A.167, N.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain B: H.120, D.127, E.156, H.162 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.120, B:D.127, B:D.127, B:H.162

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 3 residues within 4Å: Chain B: E.69, E.70, D.109 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.70 CA.12: 5 residues within 4Å: Chain B: E.69, E.70, D.75, T.105, E.106 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.69, B:E.69, B:D.75, B:D.75, B:T.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, X. et al., Structural basis for the recognition of Sonic Hedgehog by human Patched1. Science (2018)

Release Date

2018-07-11

Peptides

Protein patched homolog 1: 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

Sonic hedgehog protein

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