SMTL ID : 6bwd.1

3.7 angstrom cryoEM structure of truncated mouse TRPM7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: E.702 Chain B: E.702 Chain D: E.702 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: Y.740 Chain B: Y.740 Chain C: Y.740 Chain D: Y.740 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain B: F.700 Chain D: F.700, Y.740 No protein-ligand interaction detected (PLIP)

20 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 10 residues within 4Å: Chain A: Y.414, F.511, W.512, L.519, F.634, L.635, V.637, N.638 Chain D: L.667 Ligands: Y01.8 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:L.667, A:Y.414, A:Y.414, A:F.511, A:W.512, A:W.512, A:L.519, A:L.519, A:V.637, A:N.638 Y01.4: 6 residues within 4Å: Chain A: G.520, M.523, L.524, F.527, Q.540 Ligands: Y01.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.523, A:L.524, A:F.527, A:F.527 Y01.5: 12 residues within 4Å: Chain A: L.667, P.683, S.684, W.685, A.688 Chain B: L.519, L.522, M.523, T.526, F.527, Y.628 Ligands: Y01.12 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.667, A:W.685, A:W.685, A:A.688, B:L.519, B:L.522, B:T.526, B:F.527 Hydrogen bonds: A:S.684 Y01.6: 15 residues within 4Å: Chain A: Y.578, F.579, V.629, L.632, V.645, M.646, I.648, G.649, K.650 Chain D: V.665, S.668, F.669, V.734, V.738 Ligands: Y01.7 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Y.578, A:F.579, A:L.632, A:V.645, A:I.648, D:V.665, D:F.669, D:V.734, D:V.738 Salt bridges: A:K.650 Y01.7: 7 residues within 4Å: Chain A: Y.578, F.579, S.582, I.625, F.626, V.629 Ligands: Y01.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.578, A:F.579, A:I.625, A:I.625, A:F.626, A:F.626, A:V.629 Y01.8: 11 residues within 4Å: Chain A: M.523, T.526, F.527, Y.628 Chain D: L.667, P.683, W.685, L.687, I.691 Ligands: Y01.3, Y01.4 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.527, A:Y.628, D:L.667, D:P.683, D:W.685, D:W.685, D:L.687, D:I.691 Hydrogen bonds: D:S.684 Y01.11: 5 residues within 4Å: Chain A: P.683 Chain B: M.523, L.524, F.527, Q.540 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.523, B:L.524, B:F.527, B:F.527 Hydrogen bonds: B:Q.540 Y01.12: 11 residues within 4Å: Chain A: L.664, L.667 Chain B: Y.414, F.511, W.512, L.519, F.634, L.635, V.637, N.638 Ligands: Y01.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.511, B:W.512, B:W.512, B:L.519, B:L.519, B:V.637, B:N.638 Y01.13: 16 residues within 4Å: Chain A: V.665, S.668, F.669, L.731, V.734, V.738 Chain B: Y.578, F.579, I.625, V.629, L.632, V.645, M.646, G.649, Q.769 Ligands: Y01.14 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.625, B:V.629, B:V.629, B:L.632, A:V.665, A:F.669, A:V.734, A:V.734, A:V.738 Hydrogen bonds: B:Q.769 Y01.14: 7 residues within 4Å: Chain A: F.730 Chain B: Y.578, S.582, I.625, F.626, V.629 Ligands: Y01.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.578, B:I.625, B:I.625, B:F.626, B:F.626, B:V.629 Y01.15: 6 residues within 4Å: Chain C: G.520, M.523, L.524, F.527, Q.540 Ligands: Y01.16 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.524, C:F.527 Y01.16: 8 residues within 4Å: Chain B: P.683, W.685, L.687, I.691 Chain C: L.519, L.522, Y.628 Ligands: Y01.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.685, B:L.687, B:I.691, C:L.519, C:L.522, C:Y.628 Y01.17: 8 residues within 4Å: Chain B: L.667 Chain C: Y.414, F.511, W.512, F.634, L.635, V.637, N.638 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.414, C:F.511, C:W.512, C:W.512, C:L.635, C:V.637, C:N.638, B:L.667 Y01.18: 11 residues within 4Å: Chain C: L.667, P.683, W.685, L.687, A.688 Chain D: M.523, T.526, F.527, Y.628 Ligands: Y01.19, Y01.24 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.683, C:W.685, C:L.687, C:A.688, D:M.523, D:F.527, D:Y.628 Y01.19: 9 residues within 4Å: Chain C: V.660, L.667 Chain D: F.511, W.512, F.634, L.635, V.637, N.638 Ligands: Y01.18 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.511, D:W.512, D:W.512, D:L.635, D:N.638, C:V.660, C:L.667 Y01.20: 13 residues within 4Å: Chain B: V.665, S.668, F.669, V.738 Chain C: Y.578, F.579, L.632, V.645, M.646, I.648, G.649, Q.769 Ligands: Y01.21 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.578, C:L.632, C:I.648, B:V.665, B:V.665, B:F.669, B:V.738 Hydrogen bonds: C:Q.769 Y01.21: 10 residues within 4Å: Chain B: L.727, F.730, L.731, V.734 Chain C: Y.578, S.582, I.625, F.626, V.629 Ligands: Y01.20 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.625, C:F.626, C:F.626, C:F.626, C:V.629, B:L.731, B:V.734 Y01.22: 16 residues within 4Å: Chain C: V.665, S.668, F.669, L.731, V.734, V.738 Chain D: Y.578, F.579, I.625, V.629, L.632, V.645, M.646, G.649, Q.769 Ligands: Y01.25 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.665, C:V.665, C:F.669, C:L.731, C:V.734, C:V.738, D:Y.578, D:I.625, D:V.629, D:V.629, D:L.632 Hydrogen bonds: D:Q.769 Y01.24: 6 residues within 4Å: Chain D: G.520, M.523, L.524, F.527, Q.540 Ligands: Y01.18 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.524 Hydrogen bonds: D:Q.540 Y01.25: 10 residues within 4Å: Chain C: L.731, V.734 Chain D: Y.578, F.579, S.582, L.622, I.625, F.626, V.629 Ligands: Y01.22 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.578, D:L.622, D:I.625, D:I.625, D:F.626, D:F.626, D:V.629, C:L.731, C:V.734

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, J. et al., Structure of the mammalian TRPM7, a magnesium channel required during embryonic development. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-08-15

Peptides

Transient receptor potential cation channel subfamily M member 7: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily M member 7