SMTL ID : 7rpk.1

Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

26 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 8 residues within 4Å: Chain A: Y.11, S.428, L.431, Q.432, A.435, V.479 Ligands: Y01.3, Y01.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.11, A:L.431, A:A.435, A:V.479 Y01.2: 12 residues within 4Å: Chain A: I.343, I.347, V.350, Y.351, K.353, V.527, S.531, S.910, M.914, L.917 Ligands: Y01.6, Y01.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.343, A:I.343, A:I.347, A:V.350, A:Y.351, A:V.527, A:L.917 Hydrogen bonds: A:S.910 Salt bridges: A:K.353 Y01.3: 9 residues within 4Å: Chain A: R.9, S.10, Y.11, L.14, C.26, L.29, V.476 Ligands: Y01.1, Y01.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.11, A:Y.11, A:L.14, A:L.29, A:V.476 Y01.4: 11 residues within 4Å: Chain A: M.571, L.573, Y.766, E.767, S.810, L.814, M.817, A.846, I.849, F.850, L.863 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.571, A:L.814, A:I.849, A:I.849, A:F.850, A:L.863 Salt bridges: A:K.572 Y01.5: 4 residues within 4Å: Chain A: F.920, M.927 Ligands: Y01.8, Y01.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.920 Y01.6: 13 residues within 4Å: Chain A: A.530, S.531, I.533, F.534, A.913, A.916, L.917, F.920, C.946, W.949 Ligands: Y01.2, Y01.8, Y01.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.530, A:I.533, A:F.534, A:F.534, A:A.913, A:F.920, A:W.949 Y01.7: 10 residues within 4Å: Chain A: V.20, T.27, F.356, M.360, F.363, W.481, Y.492, I.496 Ligands: Y01.15, Y01.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.20, A:F.356, A:F.363, A:Y.492, A:Y.492 Y01.8: 6 residues within 4Å: Chain A: L.859, F.920, T.939, C.946 Ligands: Y01.5, Y01.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.859, A:L.859, A:F.920, A:T.939 Y01.9: 8 residues within 4Å: Chain A: L.346, C.349, V.350, K.353, F.497, C.520, R.521 Ligands: Y01.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.346, A:F.497, A:F.497 Salt bridges: A:R.521 Y01.10: 6 residues within 4Å: Chain A: Q.432, F.439, Y.475, V.476 Ligands: Y01.1, Y01.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.439, A:F.439, A:Y.475, A:V.476 Hydrogen bonds: A:Q.432 Y01.11: 8 residues within 4Å: Chain A: P.44, F.46, Q.327, L.331, L.369, I.370, Y.373 Ligands: AV0.28 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.46, A:L.331, A:L.369, A:I.370, A:Y.373 Hydrogen bonds: A:Q.327 Y01.12: 9 residues within 4Å: Chain A: L.436, F.439, F.443, L.830, W.833, R.890, F.974 Ligands: Y01.10, Y01.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.439, A:F.443, A:F.443, A:L.830 Salt bridges: A:R.890 Y01.13: 6 residues within 4Å: Chain A: S.855, L.858, L.859, C.946, A.950 Ligands: Y01.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.859, A:A.950 Y01.14: 5 residues within 4Å: Chain A: V.371, F.374, L.477 Ligands: Y01.3, 6OE.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.371, A:V.371, A:L.477 Y01.15: 10 residues within 4Å: Chain A: S.354, M.355, F.356, L.359, M.362, F.363, H.489 Ligands: Y01.7, Y01.9, Y01.24 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.359, A:L.359, A:M.362 Hydrogen bonds: A:M.355, A:F.356 Salt bridges: A:H.489 Y01.16: 8 residues within 4Å: Chain A: R.585, S.587, V.921, A.924, M.925, M.927 Ligands: Y01.2, Y01.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.921 Hydrogen bonds: A:S.587 Salt bridges: A:R.585 Y01.17: 5 residues within 4Å: Chain A: I.542, C.946, W.949 Ligands: Y01.6, Y01.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.542, A:W.949 Y01.18: 8 residues within 4Å: Chain A: C.541, I.542, F.546, W.550, W.553, F.954 Ligands: Y01.13, Y01.17 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.542, A:F.546, A:W.550, A:W.550, A:W.553, A:F.954 Y01.19: 7 residues within 4Å: Chain A: V.20, V.21, G.24, M.25, T.27, V.31 Ligands: Y01.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.20, A:V.21, A:T.27, A:V.31 Y01.20: 8 residues within 4Å: Chain A: F.443, Y.450, A.451, Y.453, V.454, V.823 Ligands: Y01.12, 6OE.31 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.443, A:Y.450, A:Y.453, A:V.454 Salt bridges: A:R.461 Y01.21: 7 residues within 4Å: Chain A: I.835, T.968, G.970, Q.971, I.972, P.973 Ligands: Y01.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.835, A:I.972 Hydrogen bonds: A:G.970, A:Q.971 Y01.22: 10 residues within 4Å: Chain A: I.836, L.839, Y.840, V.843, R.897, L.963, Q.966, C.969 Ligands: Y01.23, Y01.25 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.836, A:L.839, A:V.843, A:L.963 Salt bridges: A:R.897 Y01.23: 5 residues within 4Å: Chain A: I.835, L.839, C.969 Ligands: Y01.21, Y01.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.835, A:I.835, A:L.839 Y01.24: 4 residues within 4Å: Chain A: V.335, A.338 Ligands: Y01.15, AV0.28 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.335, A:A.338 Y01.25: 9 residues within 4Å: Chain A: Y.548, T.558, V.843, A.846, L.959, C.962, L.963 Ligands: Y01.22, Y01.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.548, A:T.558, A:V.843, A:A.846, A:L.959 Y01.26: 4 residues within 4Å: Chain A: Y.548, I.552, L.555 Ligands: Y01.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.548, A:I.552, A:L.555

2 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.27: 16 residues within 4Å: Chain A: Q.674, F.677, T.678, F.681, T.684, F.685, Q.687, W.688, E.690, N.691, A.722, I.723, L.726, T.730, Y.732, P.739 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.678, A:F.685, A:A.722, A:L.726, A:Y.732, A:Y.732 Hydrogen bonds: A:Q.674, A:Q.687, A:E.690, A:E.690, A:N.691 AV0.28: 9 residues within 4Å: Chain A: L.331, M.332, T.334, V.335, A.338, I.341, I.366 Ligands: Y01.11, Y01.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.341, A:I.366 Hydrogen bonds: A:M.332

2 x NA: SODIUM ION(Non-functional Binders)

NA.29: 5 residues within 4Å: Chain A: T.441, T.444, T.445, G.876, D.880 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.445, A:L.877 NA.30: 6 residues within 4Å: Chain A: G.398, I.399, D.402, A.915, T.918, T.919 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.402, A:T.919, A:T.919

1 x 6OE: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate(Non-covalent)

6OE.31: 8 residues within 4Å: Chain A: F.380, F.382, Y.450, Y.453, V.465, L.631 Ligands: Y01.14, Y01.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.450, A:Y.450 Hydrogen bonds: A:Y.453

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

NAG.32: 2 residues within 4Å: Chain A: I.745, N.746 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain A: N.306, S.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.306 NAG.34: 4 residues within 4Å: Chain A: H.658, Q.661, K.662, N.665 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.661, A:K.662 Hydrogen bonds: A:N.665 NAG.35: 2 residues within 4Å: Chain A: Q.117, N.193 No protein-ligand interaction detected (PLIP) NAG.36: 3 residues within 4Å: Chain A: H.218, N.221, T.223 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.37: 8 residues within 4Å: Chain B: K.63, D.64, E.65, E.66, D.71, T.101, E.102 Ligands: CA.38 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.65, B:E.66, B:D.71, B:T.101, B:E.102 CA.38: 7 residues within 4Å: Chain B: E.65, E.66, E.102, D.105, D.107, H.109 Ligands: CA.37 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.65, B:E.66, B:E.102, B:D.105, B:D.107

1 x ZN: ZINC ION(Non-covalent)

ZN.39: 5 residues within 4Å: Chain B: H.110, H.116, D.123, E.152, H.158 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.116, B:D.123, B:D.123, B:H.158

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.40: 5 residues within 4Å: Chain A: R.107 Chain B: K.63, R.99, T.101, R.129 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.107, B:K.63, B:R.99, B:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Dispatched uses Na + flux to power release of lipid-modified Hedgehog. Nature (2021)

Release Date

2021-10-27

Peptides

Protein dispatched homolog 1: A
Sonic hedgehog protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Membrane

We predict this structure to be a membrane protein.
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Protein dispatched homolog 1

Sonic hedgehog protein

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