SMTL ID : 8srh.1

Cryo-EM structure of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

APR.1: 17 residues within 4Å: Chain A: T.148, G.149, G.150, A.151, R.152, N.153, T.184, M.189, T.248, F.268, R.275, G.297, G.298, P.299, G.300, T.301, T.304 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.148, A:G.149, A:A.151, A:R.152, A:N.153, A:T.184, A:R.275, A:G.298, A:T.301 pi-Stacking: A:F.268 APR.6: 20 residues within 4Å: Chain A: W.1264, L.1319, L.1320, G.1321, N.1326, A.1328, A.1329, D.1330, R.1360, G.1370, G.1371, F.1372, C.1424, T.1437, D.1460, F.1476, H.1479 Ligands: MG.3, MG.4, MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.1321, A:N.1326, A:A.1329, A:F.1372, A:T.1437 Salt bridges: A:R.1360, A:R.1360, A:H.1479 pi-Stacking: A:W.1264, A:F.1372 APR.10: 17 residues within 4Å: Chain B: T.148, G.149, G.150, A.151, R.152, N.153, T.184, M.189, T.248, F.268, R.275, G.297, G.298, P.299, G.300, T.301, T.304 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.148, B:G.149, B:A.151, B:R.152, B:N.153, B:T.184, B:R.275, B:G.298, B:T.301 pi-Stacking: B:F.268 APR.15: 20 residues within 4Å: Chain B: W.1264, L.1319, L.1320, G.1321, N.1326, A.1328, A.1329, D.1330, R.1360, G.1370, G.1371, F.1372, C.1424, T.1437, D.1460, F.1476, H.1479 Ligands: MG.12, MG.13, MG.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.1321, B:N.1326, B:A.1329, B:F.1372, B:T.1437 Salt bridges: B:R.1360, B:R.1360, B:H.1479 pi-Stacking: B:W.1264, B:F.1372 APR.19: 17 residues within 4Å: Chain C: T.148, G.149, G.150, A.151, R.152, N.153, T.184, M.189, T.248, F.268, R.275, G.297, G.298, P.299, G.300, T.301, T.304 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.148, C:G.149, C:A.151, C:R.152, C:N.153, C:T.184, C:R.275, C:G.298, C:T.301 pi-Stacking: C:F.268 APR.24: 20 residues within 4Å: Chain C: W.1264, L.1319, L.1320, G.1321, N.1326, A.1328, A.1329, D.1330, R.1360, G.1370, G.1371, F.1372, C.1424, T.1437, D.1460, F.1476, H.1479 Ligands: MG.21, MG.22, MG.23 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.1321, C:N.1326, C:A.1329, C:F.1372, C:T.1437 Salt bridges: C:R.1360, C:R.1360, C:H.1479 pi-Stacking: C:W.1264, C:F.1372 APR.31: 17 residues within 4Å: Chain D: T.148, G.149, G.150, A.151, R.152, N.153, T.184, M.189, T.248, F.268, R.275, G.297, G.298, P.299, G.300, T.301, T.304 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.148, D:G.149, D:A.151, D:R.152, D:N.153, D:T.184, D:R.275, D:G.298, D:T.301 pi-Stacking: D:F.268 APR.36: 20 residues within 4Å: Chain D: W.1264, L.1319, L.1320, G.1321, N.1326, A.1328, A.1329, D.1330, R.1360, G.1370, G.1371, F.1372, C.1424, T.1437, D.1460, F.1476, H.1479 Ligands: MG.33, MG.34, MG.35 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.1321, D:N.1326, D:A.1329, D:F.1372, D:T.1437 Salt bridges: D:R.1360, D:R.1360, D:H.1479 pi-Stacking: D:W.1264, D:F.1372

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

MG.2: 4 residues within 4Å: Chain A: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.850 MG.3: 4 residues within 4Å: Chain A: G.1370, D.1460 Ligands: MG.4, APR.6 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: D.1460 Ligands: MG.3, MG.5, APR.6 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Ligands: MG.4, APR.6 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.850 MG.12: 4 residues within 4Å: Chain B: G.1370, D.1460 Ligands: MG.13, APR.15 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: D.1460 Ligands: MG.12, MG.14, APR.15 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Ligands: MG.13, APR.15 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain C: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.850 MG.21: 4 residues within 4Å: Chain C: G.1370, D.1460 Ligands: MG.22, APR.24 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain C: D.1460 Ligands: MG.21, MG.23, APR.24 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Ligands: MG.22, APR.24 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain D: E.850, Q.853, N.869, D.872 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.850 MG.33: 4 residues within 4Å: Chain D: G.1370, D.1460 Ligands: MG.34, APR.36 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain D: D.1460 Ligands: MG.33, MG.35, APR.36 No protein-ligand interaction detected (PLIP) MG.35: 2 residues within 4Å: Ligands: MG.34, APR.36 No protein-ligand interaction detected (PLIP)

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 12 residues within 4Å: Chain A: F.1003, R.1012, P.1015, F.1016 Chain B: V.942, L.945, L.946, I.972, L.975, F.976, Y.979 Ligands: CLR.8 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.942, B:V.942, B:L.945, B:L.946, B:L.975, B:L.975, B:F.976, B:Y.979, B:Y.979, A:P.1015, A:F.1016, A:F.1016 Hydrogen bonds: A:R.1012, A:R.1012 CLR.8: 6 residues within 4Å: Chain A: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.7, CLR.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1016, A:F.1016 CLR.9: 6 residues within 4Å: Chain A: E.1009, M.1013 Chain B: L.878, V.898, F.905 Ligands: CLR.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.878, B:V.898, B:F.905 CLR.16: 12 residues within 4Å: Chain B: F.1003, R.1012, P.1015, F.1016 Chain C: V.942, L.945, L.946, I.972, L.975, F.976, Y.979 Ligands: CLR.17 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.942, C:V.942, C:L.945, C:L.946, C:L.975, C:L.975, C:F.976, C:Y.979, C:Y.979, B:P.1015, B:F.1016, B:F.1016 Hydrogen bonds: B:R.1012, B:R.1012 CLR.17: 6 residues within 4Å: Chain B: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.16, CLR.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.1016, B:F.1016 CLR.18: 6 residues within 4Å: Chain B: E.1009, M.1013 Chain C: L.878, V.898, F.905 Ligands: CLR.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.878, C:V.898, C:F.905 CLR.25: 12 residues within 4Å: Chain C: F.1003, R.1012, P.1015, F.1016 Chain D: V.942, L.945, L.946, I.972, L.975, F.976, Y.979 Ligands: CLR.26 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:P.1015, C:F.1016, C:F.1016, D:V.942, D:V.942, D:L.945, D:L.946, D:L.975, D:L.975, D:F.976, D:Y.979, D:Y.979 Hydrogen bonds: C:R.1012, C:R.1012 CLR.26: 6 residues within 4Å: Chain C: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.25, CLR.27 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.1016, C:F.1016 CLR.27: 6 residues within 4Å: Chain C: E.1009, M.1013 Chain D: L.878, V.898, F.905 Ligands: CLR.26 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.878, D:V.898, D:F.905 CLR.28: 12 residues within 4Å: Chain A: V.942, L.945, L.946, I.972, L.975, F.976, Y.979 Chain D: F.1003, R.1012, P.1015, F.1016 Ligands: CLR.29 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:V.942, A:V.942, A:L.945, A:L.946, A:L.975, A:L.975, A:F.976, A:Y.979, A:Y.979, D:P.1015, D:F.1016, D:F.1016 Hydrogen bonds: D:R.1012, D:R.1012 CLR.29: 6 residues within 4Å: Chain D: E.1009, R.1012, M.1013, F.1016 Ligands: CLR.28, CLR.30 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.1016, D:F.1016 CLR.30: 6 residues within 4Å: Chain A: L.878, V.898, F.905 Chain D: E.1009, M.1013 Ligands: CLR.29 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.878, A:V.898, A:F.905

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
B

C
C

D
D

Membrane

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

TRPM2 chanzyme

Related Entries With Identical Sequence