SMTL ID : 7rpi.1

Cryo-EM structure of murine Dispatched 'T' conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

26 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 7 residues within 4Å: Chain A: Y.11, 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: 13 residues within 4Å: Chain A: I.343, I.347, V.350, Y.351, D.409, V.527, S.528, S.531, R.532, S.910, M.914 Ligands: Y01.6, Y01.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.343, A:I.347, A:V.350, A:V.350, A:Y.351, A:V.527 Hydrogen bonds: A:S.531, A:S.910 Salt bridges: A:R.532 Y01.3: 10 residues within 4Å: Chain A: F.7, R.9, Y.11, L.14, M.25, C.26, V.476, T.480 Ligands: Y01.1, Y01.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.7, A:Y.11, A:Y.11, A:L.14, A:V.476, A:T.480 Salt bridges: A:R.9 Y01.4: 12 residues within 4Å: Chain A: V.565, M.571, K.572, L.573, Y.766, E.767, L.814, M.817, A.846, I.849, F.850, L.863 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.565, A:M.571, A:L.814, A:L.814, A:I.849, A:I.849, A:F.850, A:F.850, A:L.863 Hydrogen bonds: A:L.573 Y01.5: 6 residues within 4Å: Chain A: R.585, F.920, V.921, M.927 Ligands: Y01.8, Y01.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.920, A:V.921 Hydrogen bonds: A:R.585 Y01.6: 12 residues within 4Å: Chain A: A.530, F.534, A.913, M.914, A.916, F.920, M.945, C.946, W.949 Ligands: Y01.2, Y01.8, Y01.17 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 Y01.7: 7 residues within 4Å: Chain A: V.20, T.27, M.360, F.363, W.481, Y.492 Ligands: Y01.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.20, A:T.27, A:F.363, A:W.481, A:Y.492, A:Y.492, A:Y.492 Y01.8: 8 residues within 4Å: Chain A: L.859, F.920, T.939, L.943, C.946 Ligands: Y01.5, Y01.6, Y01.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.859, A:F.920, A:F.920, A:L.943 Y01.9: 7 residues within 4Å: Chain A: L.346, V.350, K.353, F.497, C.520, R.521, L.524 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.346, A:V.350, A:F.497, A:L.524 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: 11 residues within 4Å: Chain A: L.43, P.44, F.46, Q.327, L.369, Y.373, F.385, N.389, L.390, Y.466 Ligands: AV0.27 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.43, A:P.44, A:L.369, A:Y.373, A:F.385, A:Y.466 Hydrogen bonds: A:Q.327 Y01.12: 8 residues within 4Å: Chain A: L.436, F.439, F.443, L.830, W.833, R.890 Ligands: Y01.10, Y01.20 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.436, A:L.436, A:F.439, A:F.443, A:F.443, A:F.443, A:L.830, A:W.833 Salt bridges: A:R.890 Y01.13: 12 residues within 4Å: Chain A: F.554, L.557, S.855, L.858, L.859, L.943, C.946, V.947, A.950, F.951 Ligands: Y01.17, Y01.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.554, A:L.557, A:L.858, A:L.859, A:L.943, A:V.947, A:A.950, A:F.951 Y01.14: 6 residues within 4Å: Chain A: L.29, V.371, V.473, V.476, L.477 Ligands: Y01.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.29, A:V.371, A:V.473, A:V.476, A:L.477 Y01.15: 11 residues within 4Å: Chain A: S.354, M.355, F.356, L.359, M.362, F.363, H.489, L.493, F.497 Ligands: Y01.7, Y01.24 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.359, A:L.359, A:L.359, A:F.497 Hydrogen bonds: A:M.355, A:F.356 Salt bridges: A:H.489 Y01.16: 9 residues within 4Å: Chain A: R.585, V.921, A.924, M.927, P.928, S.929, T.930 Ligands: Y01.2, Y01.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.921, A:M.927 Salt bridges: A:R.585 Y01.17: 9 residues within 4Å: Chain A: V.538, I.542, C.946, W.949, A.950 Ligands: Y01.6, Y01.8, Y01.13, Y01.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.538, A:I.542, A:W.949, A:A.950 Y01.18: 9 residues within 4Å: Chain A: C.541, I.542, F.546, W.550, W.553, A.950, 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.553, A:A.950, A:F.954 Y01.19: 7 residues within 4Å: Chain A: D.17, W.18, V.20, V.21, G.24, T.27, L.28 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.20, A:V.21, A:L.28 Y01.20: 8 residues within 4Å: Chain A: F.443, Y.450, A.451, Y.453, V.454, R.461, V.823 Ligands: Y01.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.443, A:F.443, A:Y.450, A:V.454 Salt bridges: A:R.461 Y01.21: 8 residues within 4Å: Chain A: I.835, T.968, C.969, 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, A:I.972 Hydrogen bonds: A:Q.971 Y01.22: 10 residues within 4Å: Chain A: I.836, L.839, Y.840, R.897, L.963, G.964, Q.966, C.969 Ligands: Y01.23, Y01.25 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.836, A:L.839, A:L.963, A:L.963 Hydrogen bonds: A:Q.966 Salt bridges: A:R.897 Y01.23: 4 residues within 4Å: Chain A: I.835, C.969 Ligands: Y01.21, Y01.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.835, A:I.835 Y01.24: 5 residues within 4Å: Chain A: A.338, A.342, I.366 Ligands: Y01.15, AV0.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.342, A:I.366 Y01.25: 8 residues within 4Å: Chain A: L.555, T.558, V.843, A.846, L.959, L.963 Ligands: Y01.22, Y01.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.555, A:T.558, A:V.843, A:A.846, A:L.959 Y01.26: 3 residues within 4Å: Chain A: Y.548, I.552 Ligands: Y01.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.548, A:I.552

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

AV0.27: 10 residues within 4Å: Chain A: M.332, D.333, T.334, V.335, Y.336, A.338, I.366, L.393 Ligands: Y01.11, Y01.24 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.366, A:L.393 Hydrogen bonds: A:D.333, A:D.333, A:Y.336 AV0.28: 16 residues within 4Å: Chain A: F.677, T.678, F.681, T.684, F.685, Q.687, W.688, N.691, I.719, A.722, I.723, L.726, T.730, G.731, Y.732, P.739 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.677, A:F.681, A:T.684, A:I.719, A:A.722, A:L.726, A:L.726, A:T.730, A:Y.732 Hydrogen bonds: A:Q.674, A:Q.687, A:G.731

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

NAG.29: 2 residues within 4Å: Chain A: I.745, N.746 No protein-ligand interaction detected (PLIP) NAG.30: 4 residues within 4Å: Chain A: H.658, Q.661, K.662, N.665 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.661 Hydrogen bonds: A:N.665 NAG.31: 3 residues within 4Å: Chain A: N.306, S.308, G.310 No protein-ligand interaction detected (PLIP) NAG.32: 2 residues within 4Å: Chain A: N.221, T.223 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.223 NAG.33: 2 residues within 4Å: Chain A: Q.117, N.193 No protein-ligand interaction detected (PLIP)

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

NA.34: 6 residues within 4Å: Chain A: T.441, T.444, T.445, G.876, L.877, D.880 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.444, A:G.876 Water bridges: A:T.445 NA.35: 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:T.441, A:T.441, A:S.442 Water bridges: A:D.403, A:S.442

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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