SMTL ID : 8sre.1

Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)

APR.1: 18 residues within 4Å: Chain A: T.148, G.149, G.150, A.151, R.152, N.153, T.184, T.186, M.189, T.248, F.268, E.271, R.275, G.298, P.299, G.300, T.301, T.304 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.148, A:G.149, A:A.151, A:R.152, A:N.153, A:N.153, A:R.275, A:G.298, A:G.298, A:G.300, A:T.301, A:T.304 Salt bridges: A:R.275 pi-Stacking: A:F.268 APR.8: 24 residues within 4Å: Chain A: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, A.1328, D.1330, R.1360, G.1370, G.1371, F.1372, E.1386, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: MG.4, MG.5, MG.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:W.1264, A:G.1321, A:N.1326, A:D.1330, A:F.1372, A:D.1426, A:D.1460 Water bridges: A:G.1370, A:E.1390, A:E.1390, A:D.1460 Salt bridges: A:R.1360, A:R.1428, A:R.1428 pi-Stacking: A:W.1264, A:W.1264, A:W.1264, A:F.1372 APR.14: 18 residues within 4Å: Chain B: T.148, G.149, G.150, A.151, R.152, N.153, T.184, T.186, M.189, T.248, F.268, E.271, R.275, G.298, P.299, G.300, T.301, T.304 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.148, B:G.149, B:A.151, B:R.152, B:N.153, B:N.153, B:R.275, B:G.298, B:G.298, B:G.300, B:T.301, B:T.304 Salt bridges: B:R.275 pi-Stacking: B:F.268 APR.21: 24 residues within 4Å: Chain B: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, A.1328, D.1330, R.1360, G.1370, G.1371, F.1372, E.1386, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: MG.17, MG.18, MG.19 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:W.1264, B:G.1321, B:N.1326, B:D.1330, B:F.1372, B:D.1426, B:D.1460 Water bridges: B:G.1370, B:E.1390, B:E.1390, B:D.1460 Salt bridges: B:R.1360, B:R.1428, B:R.1428 pi-Stacking: B:W.1264, B:W.1264, B:W.1264, B:F.1372 APR.22: 18 residues within 4Å: Chain C: T.148, G.149, G.150, A.151, R.152, N.153, T.184, T.186, M.189, T.248, F.268, E.271, R.275, G.298, P.299, G.300, T.301, T.304 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.148, C:G.149, C:A.151, C:R.152, C:N.153, C:N.153, C:R.275, C:G.298, C:G.298, C:G.300, C:T.301, C:T.304 Salt bridges: C:R.275 pi-Stacking: C:F.268 APR.29: 24 residues within 4Å: Chain C: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, A.1328, D.1330, R.1360, G.1370, G.1371, F.1372, E.1386, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: MG.25, MG.26, MG.27 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:W.1264, C:G.1321, C:N.1326, C:D.1330, C:F.1372, C:D.1426, C:D.1460 Water bridges: C:G.1370, C:E.1390, C:E.1390, C:D.1460 Salt bridges: C:R.1360, C:R.1428, C:R.1428 pi-Stacking: C:W.1264, C:W.1264, C:W.1264, C:F.1372 APR.34: 18 residues within 4Å: Chain D: T.148, G.149, G.150, A.151, R.152, N.153, T.184, T.186, M.189, T.248, F.268, E.271, R.275, G.298, P.299, G.300, T.301, T.304 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.148, D:G.149, D:A.151, D:R.152, D:N.153, D:N.153, D:R.275, D:G.298, D:G.298, D:G.300, D:T.301, D:T.304 Salt bridges: D:R.275 pi-Stacking: D:F.268 APR.41: 24 residues within 4Å: Chain D: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, A.1328, D.1330, R.1360, G.1370, G.1371, F.1372, E.1386, E.1390, C.1424, D.1426, R.1428, V.1435, D.1460, F.1476, H.1479 Ligands: MG.37, MG.38, MG.39 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:W.1264, D:G.1321, D:N.1326, D:D.1330, D:F.1372, D:D.1426, D:D.1460 Water bridges: D:G.1370, D:E.1390, D:E.1390, D:D.1460 Salt bridges: D:R.1360, D:R.1428, D:R.1428 pi-Stacking: D:W.1264, D:W.1264, D:W.1264, D:F.1372

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

MG.2: 5 residues within 4Å: Chain A: E.850, Q.853, N.869, D.872, R.913 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.850, A:D.872 MG.3: 5 residues within 4Å: Chain A: L.621, I.622, G.623, S.626, E.1114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.621, A:G.623, A:E.1114, A:E.1114 MG.4: 4 residues within 4Å: Chain A: G.1370, E.1390 Ligands: MG.5, APR.8 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.1370, A:E.1390, A:E.1390, H2O.1, H2O.1 MG.5: 6 residues within 4Å: Chain A: E.1386, E.1390, D.1459 Ligands: MG.4, MG.6, APR.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.1386, A:E.1390 MG.6: 3 residues within 4Å: Chain A: E.1386 Ligands: MG.5, APR.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.1386, A:E.1386 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain B: E.850, Q.853, N.869, D.872, R.913 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.850, B:D.872 MG.16: 5 residues within 4Å: Chain B: L.621, I.622, G.623, S.626, E.1114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:L.621, B:G.623, B:E.1114, B:E.1114 MG.17: 4 residues within 4Å: Chain B: G.1370, E.1390 Ligands: MG.18, APR.21 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.1370, B:E.1390, B:E.1390, H2O.1, H2O.1 MG.18: 6 residues within 4Å: Chain B: E.1386, E.1390, D.1459 Ligands: MG.17, MG.19, APR.21 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.1386, B:E.1390 MG.19: 3 residues within 4Å: Chain B: E.1386 Ligands: MG.18, APR.21 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.1386, B:E.1386 MG.23: 5 residues within 4Å: Chain C: E.850, Q.853, N.869, D.872, R.913 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.850, C:D.872 MG.24: 5 residues within 4Å: Chain C: L.621, I.622, G.623, S.626, E.1114 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:L.621, C:G.623, C:E.1114, C:E.1114 MG.25: 4 residues within 4Å: Chain C: G.1370, E.1390 Ligands: MG.26, APR.29 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.1370, C:E.1390, C:E.1390, H2O.1, H2O.1 MG.26: 6 residues within 4Å: Chain C: E.1386, E.1390, D.1459 Ligands: MG.25, MG.27, APR.29 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.1386, C:E.1390 MG.27: 3 residues within 4Å: Chain C: E.1386 Ligands: MG.26, APR.29 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.1386, C:E.1386 MG.35: 5 residues within 4Å: Chain D: E.850, Q.853, N.869, D.872, R.913 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.850, D:D.872 MG.36: 5 residues within 4Å: Chain D: L.621, I.622, G.623, S.626, E.1114 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:L.621, D:G.623, D:E.1114, D:E.1114 MG.37: 4 residues within 4Å: Chain D: G.1370, E.1390 Ligands: MG.38, APR.41 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.1370, D:E.1390, D:E.1390, H2O.1, H2O.1 MG.38: 6 residues within 4Å: Chain D: E.1386, E.1390, D.1459 Ligands: MG.37, MG.39, APR.41 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.1386, D:E.1390 MG.39: 3 residues within 4Å: Chain D: E.1386 Ligands: MG.38, APR.41 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.1386, D:E.1386

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 8 residues within 4Å: Chain A: L.878, V.898, I.902, F.905 Chain B: E.1009, T.1010, M.1013 Ligands: CLR.13 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.878, A:V.898, A:I.902, A:F.905, A:F.905, B:T.1010 CLR.9: 14 residues within 4Å: Chain A: F.1003, R.1012, P.1015, F.1016, A.1019 Chain C: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Ligands: CLR.10 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:V.942, C:L.945, C:L.949, C:F.976, C:Y.979, C:Y.979, C:Y.979, A:F.1003, A:P.1015, A:P.1015, A:F.1016, A:A.1019 Hydrogen bonds: A:R.1012, A:R.1012 CLR.10: 6 residues within 4Å: Chain A: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.9, CLR.28 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1016, A:F.1016, A:F.1016 Hydrogen bonds: A:E.1009 CLR.12: 14 residues within 4Å: Chain A: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Chain B: F.1003, R.1012, P.1015, F.1016, A.1019 Ligands: CLR.13 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.942, A:L.945, A:L.949, A:F.976, A:Y.979, A:Y.979, A:Y.979, B:F.1003, B:P.1015, B:F.1016, B:A.1019 Hydrogen bonds: B:R.1012, B:R.1012 CLR.13: 6 residues within 4Å: Chain B: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.7, CLR.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.1016, B:F.1016, B:F.1016 Hydrogen bonds: B:E.1009 CLR.20: 8 residues within 4Å: Chain B: L.878, V.898, I.902, F.905 Chain D: E.1009, T.1010, M.1013 Ligands: CLR.33 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.878, B:V.898, B:I.902, B:F.905, B:F.905, D:T.1010 CLR.28: 8 residues within 4Å: Chain A: E.1009, T.1010, M.1013 Chain C: L.878, V.898, I.902, F.905 Ligands: CLR.10 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.878, C:V.898, C:I.902, C:F.905, C:F.905, A:T.1010 CLR.30: 14 residues within 4Å: Chain C: F.1003, R.1012, P.1015, F.1016, A.1019 Chain D: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Ligands: CLR.31 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:F.1003, C:P.1015, C:P.1015, C:F.1016, C:A.1019, D:V.942, D:L.945, D:L.949, D:F.976, D:Y.979, D:Y.979, D:Y.979 Hydrogen bonds: C:R.1012, C:R.1012 CLR.31: 6 residues within 4Å: Chain C: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.30, CLR.40 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.1016, C:F.1016, C:F.1016 Hydrogen bonds: C:E.1009 CLR.32: 14 residues within 4Å: Chain B: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979 Chain D: F.1003, R.1012, P.1015, F.1016, A.1019 Ligands: CLR.33 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:V.942, B:L.945, B:L.949, B:F.976, B:Y.979, B:Y.979, B:Y.979, D:F.1003, D:P.1015, D:P.1015, D:F.1016, D:A.1019 Hydrogen bonds: D:R.1012, D:R.1012 CLR.33: 6 residues within 4Å: Chain D: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.20, CLR.32 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.1016, D:F.1016, D:F.1016 Hydrogen bonds: D:E.1009 CLR.40: 8 residues within 4Å: Chain C: E.1009, T.1010, M.1013 Chain D: L.878, V.898, I.902, F.905 Ligands: CLR.31 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.878, D:V.898, D:I.902, D:F.905, D:F.905, C:T.1010

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y. et al., Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. To Be Published

Release Date

2024-05-15

Peptides

TRPM2 chanzyme: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

TRPM2 chanzyme

Related Entries With Identical Sequence