SMTL ID : 7rph.1

Cryo-EM structure of murine Dispatched 'R' conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: T.441, T.444, T.445, G.876, V.879, D.880 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.444, A:T.445, A:D.880 Water bridges: A:T.445 NA.2: 6 residues within 4Å: Chain A: G.398, I.399, D.402, A.915, T.918, T.919 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.918, A:T.918 Water bridges: A:G.400, A:T.919 NA.3: 4 residues within 4Å: Chain A: D.403, M.438, T.441, S.442 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.403, A:T.441 Water bridges: A:D.403, A:D.403, A:S.442

26 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 9 residues within 4Å: Chain A: Y.11, L.431, Q.432, A.435, Y.475, V.479, T.480 Ligands: Y01.13, Y01.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.11, A:Y.11, A:L.431, A:Q.432, A:A.435, A:V.479, A:T.480 Y01.5: 9 residues within 4Å: Chain A: L.346, V.350, Y.351, V.527, S.531, S.910, M.914, L.917 Ligands: Y01.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.346, A:V.350, A:Y.351, A:Y.351, A:V.527, A:L.917 Hydrogen bonds: A:Y.351, A:S.531, A:S.910 Water bridges: A:Y.351 Salt bridges: A:K.353 Y01.6: 8 residues within 4Å: Chain A: F.7, P.8, R.9, L.14, M.25, C.26, T.480 Ligands: Y01.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.7, A:L.14 Salt bridges: A:R.9, A:R.9 Y01.7: 11 residues within 4Å: Chain A: V.565, M.571, K.572, L.573, Y.766, L.814, M.817, A.846, I.849, F.850, L.863 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.565, A:M.571, A:L.814, A:A.846, A:I.849, A:F.850, A:L.863 Hydrogen bonds: A:L.573 Y01.8: 8 residues within 4Å: Chain A: R.585, F.920, M.927, T.935, T.939, M.942 Ligands: Y01.11, Y01.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.920, A:F.920 Hydrogen bonds: A:T.935, A:T.939 Salt bridges: A:R.585 Y01.9: 12 residues within 4Å: Chain A: A.530, S.531, F.534, A.913, M.914, A.916, F.920, M.945, C.946, W.949 Ligands: Y01.11, Y01.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.534, A:F.534, A:A.913, A:F.920, A:M.945, A:W.949 Y01.10: 8 residues within 4Å: Chain A: T.27, F.356, M.360, F.363, W.481, Y.492, I.496 Ligands: Y01.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.27, A:F.356, A:F.363, A:Y.492 Y01.11: 7 residues within 4Å: Chain A: L.859, F.920, T.939, C.946 Ligands: Y01.8, Y01.9, Y01.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.859, A:L.859, A:F.920, A:T.939 Hydrogen bonds: A:S.586 Water bridges: A:Q.582 Y01.12: 8 residues within 4Å: Chain A: L.346, C.349, V.350, K.353, C.520, R.521, L.524 Ligands: Y01.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.350 Salt bridges: A:R.521 Y01.13: 6 residues within 4Å: Chain A: Q.432, F.439, Y.475, V.476 Ligands: Y01.4, Y01.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.439, A:F.439, A:Y.475, A:V.476 Y01.14: 10 residues within 4Å: Chain A: D.45, F.46, Q.327, L.331, I.366, L.369, I.370, Y.373, F.385 Ligands: AV0.31 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.46, A:L.331, A:I.366, A:L.369, A:L.369, A:I.370, A:Y.373, A:Y.373, A:F.385 Hydrogen bonds: A:D.45, A:Q.327 Y01.15: 11 residues within 4Å: Chain A: L.436, F.439, V.440, F.443, V.827, L.830, W.833, R.890, F.974 Ligands: Y01.13, Y01.23 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.436, A:L.436, A:F.439, A:V.440, A:F.443, A:V.827, A:W.833, A:F.974 Salt bridges: A:R.890 Y01.16: 11 residues within 4Å: Chain A: W.553, F.554, L.557, S.855, L.858, L.859, C.946, V.947 Ligands: Y01.11, Y01.20, Y01.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.557, A:L.858, A:L.858, A:V.947 Y01.17: 8 residues within 4Å: Chain A: C.26, L.29, I.30, V.371, F.374, V.379 Ligands: Y01.4, Y01.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.30, A:V.371, A:F.374, A:V.379 Y01.18: 10 residues within 4Å: Chain A: S.354, M.355, F.356, L.359, M.362, F.363, H.489, F.497 Ligands: Y01.10, Y01.27 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.359, A:L.359, A:M.362, A:F.363, A:F.497 Hydrogen bonds: A:M.355, A:F.356 Salt bridges: A:H.489 Y01.19: 7 residues within 4Å: Chain A: R.585, A.924, M.927, P.928, S.929, T.930 Ligands: Y01.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.927 Salt bridges: A:R.585 Y01.20: 5 residues within 4Å: Chain A: I.542, C.946 Ligands: Y01.9, Y01.16, Y01.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.542 Y01.21: 10 residues within 4Å: Chain A: C.541, I.542, K.545, F.546, W.550, W.553, F.554, F.954 Ligands: Y01.16, Y01.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.542, A:F.546, A:W.550, A:F.554, A:F.954 Salt bridges: A:K.545 Y01.22: 5 residues within 4Å: Chain A: V.20, V.21, T.27, L.28, V.31 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.20, A:V.21, A:T.27, A:V.31 Y01.23: 8 residues within 4Å: Chain A: F.443, Y.450, Y.453, V.454, R.461, V.823, S.826 Ligands: Y01.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.443, A:V.454, A:V.823 Salt bridges: A:R.461 Y01.24: 6 residues within 4Å: Chain A: F.825, I.835, T.968, C.969, Q.971 Ligands: Y01.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.825, A:I.835, A:I.835 Y01.25: 7 residues within 4Å: Chain A: I.836, Y.840, R.897, Q.966, C.969 Ligands: Y01.26, Y01.28 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.836, A:Y.840 Salt bridges: A:R.897 Y01.26: 4 residues within 4Å: Chain A: I.835, C.969 Ligands: Y01.24, Y01.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.835, A:I.835 Y01.27: 6 residues within 4Å: Chain A: A.338, I.339, I.341, A.342 Ligands: Y01.18, AV0.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.339, A:I.341, A:A.342 Y01.28: 9 residues within 4Å: Chain A: Y.548, T.558, V.843, A.846, L.959, C.962, L.963 Ligands: Y01.25, Y01.29 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.548, A:T.558, A:V.843, A:A.846, A:L.959, A:L.963 Y01.29: 4 residues within 4Å: Chain A: Y.548, I.552, L.555 Ligands: Y01.28 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.548, A:Y.548, A:I.552, A:L.555

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

AV0.30: 15 residues within 4Å: Chain A: F.677, F.681, F.685, Q.687, W.688, N.691, I.719, A.722, I.723, L.726, T.730, Y.732, L.734, P.739, G.740 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.677, A:F.677, A:F.681, A:F.685, A:W.688, A:I.719, A:A.722, A:L.726, A:L.726, A:T.730, A:Y.732, A:Y.732, A:L.734 Hydrogen bonds: A:N.691, A:N.691 AV0.31: 12 residues within 4Å: Chain A: L.331, M.332, D.333, T.334, V.335, Y.336, A.338, I.341, L.390, L.393 Ligands: Y01.14, Y01.27 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.331, A:I.341, A:L.393 Hydrogen bonds: A:D.333, A:D.333, A:Y.336, A:Y.336

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

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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

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