- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 4 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)
- 4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
AMP.2: 12 residues within 4Å:- Chain A: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, R.1360, F.1372, R.1428, D.1460
- Ligands: RP5.1, MG.6
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:G.1321, A:K.1322, A:N.1326, A:R.1360, A:R.1428, A:D.1460
- pi-Stacking: A:W.1264, A:W.1264, A:W.1264, A:F.1372
AMP.12: 12 residues within 4Å:- Chain B: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, R.1360, F.1372, R.1428, D.1460
- Ligands: RP5.11, MG.16
10 PLIP interactions:10 interactions with chain B- Hydrogen bonds: B:G.1321, B:K.1322, B:N.1326, B:R.1360, B:R.1428, B:D.1460
- pi-Stacking: B:W.1264, B:W.1264, B:W.1264, B:F.1372
AMP.21: 12 residues within 4Å:- Chain C: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, R.1360, F.1372, R.1428, D.1460
- Ligands: RP5.20, MG.25
10 PLIP interactions:10 interactions with chain C- Hydrogen bonds: C:G.1321, C:K.1322, C:N.1326, C:R.1360, C:R.1428, C:D.1460
- pi-Stacking: C:W.1264, C:W.1264, C:W.1264, C:F.1372
AMP.32: 12 residues within 4Å:- Chain D: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, R.1360, F.1372, R.1428, D.1460
- Ligands: RP5.31, MG.36
10 PLIP interactions:10 interactions with chain D- Hydrogen bonds: D:G.1321, D:K.1322, D:N.1326, D:R.1360, D:R.1428, D:D.1460
- pi-Stacking: D:W.1264, D:W.1264, D:W.1264, D:F.1372
- 17 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.3: 5 residues within 4Å:- Chain A: E.850, Q.853, N.869, D.872, R.913
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.850, A:E.850, A:D.872, H2O.1, H2O.1
MG.4: 4 residues within 4Å:- Chain A: L.621, I.622, G.623, E.1114
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:L.621, A:G.623, A:E.1114, H2O.1, H2O.1
MG.5: 4 residues within 4Å:- Chain A: G.1370, E.1390, D.1460
- Ligands: RP5.1
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:G.1370, A:E.1390, A:E.1390, A:D.1460, H2O.1
MG.6: 4 residues within 4Å:- Chain A: G.1371, E.1386
- Ligands: RP5.1, AMP.2
No protein-ligand interaction detected (PLIP)MG.10: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.13: 5 residues within 4Å:- Chain B: E.850, Q.853, N.869, D.872, R.913
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.850, B:E.850, B:D.872, H2O.1, H2O.1
MG.14: 4 residues within 4Å:- Chain B: L.621, I.622, G.623, E.1114
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:L.621, B:G.623, B:E.1114, H2O.1, H2O.1
MG.15: 4 residues within 4Å:- Chain B: G.1370, E.1390, D.1460
- Ligands: RP5.11
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:G.1370, B:E.1390, B:E.1390, B:D.1460, H2O.1
MG.16: 4 residues within 4Å:- Chain B: G.1371, E.1386
- Ligands: RP5.11, AMP.12
No protein-ligand interaction detected (PLIP)MG.22: 5 residues within 4Å:- Chain C: E.850, Q.853, N.869, D.872, R.913
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.850, C:E.850, C:D.872, H2O.2, H2O.2
MG.23: 4 residues within 4Å:- Chain C: L.621, I.622, G.623, E.1114
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:L.621, C:G.623, C:E.1114, H2O.2, H2O.2
MG.24: 4 residues within 4Å:- Chain C: G.1370, E.1390, D.1460
- Ligands: RP5.20
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:G.1370, C:E.1390, C:E.1390, C:D.1460, H2O.2
MG.25: 4 residues within 4Å:- Chain C: G.1371, E.1386
- Ligands: RP5.20, AMP.21
No protein-ligand interaction detected (PLIP)MG.33: 5 residues within 4Å:- Chain D: E.850, Q.853, N.869, D.872, R.913
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:E.850, D:E.850, D:D.872, H2O.2, H2O.2
MG.34: 4 residues within 4Å:- Chain D: L.621, I.622, G.623, E.1114
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:L.621, D:G.623, D:E.1114, H2O.2, H2O.2
MG.35: 4 residues within 4Å:- Chain D: G.1370, E.1390, D.1460
- Ligands: RP5.31
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:G.1370, D:E.1390, D:E.1390, D:D.1460, H2O.2
MG.36: 4 residues within 4Å:- Chain D: G.1371, E.1386
- Ligands: RP5.31, AMP.32
No protein-ligand interaction detected (PLIP)- 12 x CLR: CHOLESTEROL(Non-covalent)
CLR.7: 8 residues within 4Å:- Chain A: L.878, V.898, I.902, F.905
- Chain D: E.1009, T.1010, M.1013
- Ligands: CLR.30
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: D:T.1010, A:V.898, A:I.902, A:F.905
CLR.8: 13 residues within 4Å:- Chain A: F.1003, R.1012, P.1015, F.1016, A.1019
- Chain B: V.942, L.945, L.946, I.972, L.975, F.976, Y.979
- Ligands: CLR.9
14 PLIP interactions:6 interactions with chain B, 8 interactions with chain A- Hydrophobic interactions: B:L.945, B:L.946, B:F.976, B:Y.979, B:Y.979, B:Y.979, A:F.1003, A:P.1015, A:P.1015, A:F.1016, A:F.1016, A:A.1019
- Hydrogen bonds: A:R.1012, A:R.1012
CLR.9: 6 residues within 4Å:- Chain A: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.8, CLR.17
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.1016
- Hydrogen bonds: A:E.1009
CLR.17: 8 residues within 4Å:- Chain A: E.1009, T.1010, M.1013
- Chain B: L.878, V.898, I.902, F.905
- Ligands: CLR.9
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain B- Hydrophobic interactions: A:T.1010, B:V.898, B:I.902, B:F.905
CLR.18: 13 residues within 4Å:- Chain B: F.1003, R.1012, P.1015, F.1016, A.1019
- Chain C: V.942, L.945, L.946, I.972, L.975, F.976, Y.979
- Ligands: CLR.19
14 PLIP interactions:8 interactions with chain B, 6 interactions with chain C- Hydrophobic interactions: B:F.1003, B:P.1015, B:P.1015, B:F.1016, B:F.1016, B:A.1019, C:L.945, C:L.946, C:F.976, C:Y.979, C:Y.979, C:Y.979
- Hydrogen bonds: B:R.1012, B:R.1012
CLR.19: 6 residues within 4Å:- Chain B: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.18, CLR.26
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:F.1016
- Hydrogen bonds: B:E.1009
CLR.26: 8 residues within 4Å:- Chain B: E.1009, T.1010, M.1013
- Chain C: L.878, V.898, I.902, F.905
- Ligands: CLR.19
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:V.898, C:I.902, C:F.905, B:T.1010
CLR.27: 13 residues within 4Å:- Chain C: F.1003, R.1012, P.1015, F.1016, A.1019
- Chain D: V.942, L.945, L.946, I.972, L.975, F.976, Y.979
- Ligands: CLR.28
14 PLIP interactions:8 interactions with chain C, 6 interactions with chain D- Hydrophobic interactions: C:F.1003, C:P.1015, C:P.1015, C:F.1016, C:F.1016, C:A.1019, D:L.945, D:L.946, D:F.976, D:Y.979, D:Y.979, D:Y.979
- Hydrogen bonds: C:R.1012, C:R.1012
CLR.28: 6 residues within 4Å:- Chain C: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.27, CLR.37
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:F.1016
- Hydrogen bonds: C:E.1009
CLR.29: 13 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, A.1019
- Ligands: CLR.30
14 PLIP interactions:6 interactions with chain A, 8 interactions with chain D- Hydrophobic interactions: A:L.945, A:L.946, A:F.976, A:Y.979, A:Y.979, A:Y.979, D:F.1003, D:P.1015, D:P.1015, D:F.1016, D:F.1016, D:A.1019
- Hydrogen bonds: D:R.1012, D:R.1012
CLR.30: 6 residues within 4Å:- Chain D: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.7, CLR.29
2 PLIP interactions:2 interactions with chain D- Hydrophobic interactions: D:F.1016
- Hydrogen bonds: D:E.1009
CLR.37: 8 residues within 4Å:- Chain C: E.1009, T.1010, M.1013
- Chain D: L.878, V.898, I.902, F.905
- Ligands: CLR.28
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:V.898, D:I.902, 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. Nat.Struct.Mol.Biol. (2024)
- Release Date
- 2024-05-08
- Peptides
- TRPM2 Chanzyme: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 4 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)
- 4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
- 17 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 12 x CLR: CHOLESTEROL(Non-covalent)
- 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. Nat.Struct.Mol.Biol. (2024)
- Release Date
- 2024-05-08
- Peptides
- TRPM2 Chanzyme: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.