- 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: 17 residues within 4Å:- Chain A: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, G.1370, G.1371, F.1372, E.1386, E.1390, D.1459, D.1460
- Ligands: RP5.1, MG.6, MG.7, MG.8
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.1321, A:N.1326, A:F.1372
- pi-Stacking: A:W.1264, A:W.1264, A:F.1372
AMP.14: 17 residues within 4Å:- Chain B: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, G.1370, G.1371, F.1372, E.1386, E.1390, D.1459, D.1460
- Ligands: RP5.13, MG.18, MG.19, MG.20
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:G.1321, B:N.1326, B:F.1372, B:E.1386, B:E.1386
- pi-Stacking: B:W.1264, B:W.1264, B:F.1372
AMP.25: 17 residues within 4Å:- Chain C: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, G.1370, G.1371, F.1372, E.1386, E.1390, D.1459, D.1460
- Ligands: RP5.24, MG.29, MG.30, MG.31
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:G.1321, C:N.1326, C:F.1372, C:E.1386
- pi-Stacking: C:W.1264, C:W.1264, C:F.1372
AMP.38: 17 residues within 4Å:- Chain D: W.1264, L.1319, L.1320, G.1321, K.1322, N.1326, G.1370, G.1371, F.1372, E.1386, E.1390, D.1459, D.1460
- Ligands: RP5.37, MG.42, MG.43, MG.44
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:G.1321, D:N.1326, D:F.1372
- pi-Stacking: D:W.1264, D:W.1264, D:F.1372
- 4 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)
APR.3: 19 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.297, 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:G.149, A:A.151, A:R.152, A:N.153, A:N.153, A:T.184, A:R.275, A:G.298, A:G.300, A:T.301, A:T.301
- pi-Stacking: A:F.268
APR.15: 19 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.297, 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:G.149, B:A.151, B:R.152, B:N.153, B:N.153, B:T.184, B:R.275, B:G.298, B:G.300, B:T.301, B:T.301
- pi-Stacking: B:F.268
APR.26: 19 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.297, 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:G.149, C:A.151, C:R.152, C:N.153, C:N.153, C:T.184, C:R.275, C:G.298, C:G.300, C:T.301, C:T.301
- pi-Stacking: C:F.268
APR.39: 19 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.297, 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:G.149, D:A.151, D:R.152, D:N.153, D:N.153, D:T.184, D:R.275, D:G.298, D:G.300, D:T.301, D:T.301
- pi-Stacking: D:F.268
- 21 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 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.5: 4 residues within 4Å:- Chain A: L.621, I.622, G.623, 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.6: 6 residues within 4Å:- Chain A: G.1370, E.1390, D.1460
- Ligands: RP5.1, AMP.2, MG.7
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:G.1370, A:E.1390, A:D.1460, AMP.2
MG.7: 6 residues within 4Å:- Chain A: E.1386, E.1390, D.1459, D.1460
- Ligands: AMP.2, MG.6
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Ligand interactions- Metal complexes: A:E.1386, A:E.1390, A:D.1460, AMP.2, AMP.2
MG.8: 3 residues within 4Å:- Chain A: R.1385, E.1386
- Ligands: AMP.2
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:E.1386
MG.12: 4 residues within 4Å:- Chain A: G.984
- Chain B: G.984
- Chain C: G.984
- Chain D: G.984
No protein-ligand interaction detected (PLIP)MG.16: 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.17: 4 residues within 4Å:- Chain B: L.621, I.622, G.623, 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.18: 6 residues within 4Å:- Chain B: G.1370, E.1390, D.1460
- Ligands: RP5.13, AMP.14, MG.19
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:G.1370, B:E.1390, B:D.1460
MG.19: 6 residues within 4Å:- Chain B: E.1386, E.1390, D.1459, D.1460
- Ligands: AMP.14, MG.18
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:E.1386, B:E.1390, B:D.1460
MG.20: 3 residues within 4Å:- Chain B: R.1385, E.1386
- Ligands: AMP.14
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:E.1386
MG.27: 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.28: 4 residues within 4Å:- Chain C: L.621, I.622, G.623, 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.29: 6 residues within 4Å:- Chain C: G.1370, E.1390, D.1460
- Ligands: RP5.24, AMP.25, MG.30
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Ligand interactions- Metal complexes: C:G.1370, C:E.1390, C:D.1460, AMP.25
MG.30: 6 residues within 4Å:- Chain C: E.1386, E.1390, D.1459, D.1460
- Ligands: AMP.25, MG.29
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Ligand interactions- Metal complexes: C:E.1386, C:E.1390, C:D.1460, AMP.25, AMP.25
MG.31: 3 residues within 4Å:- Chain C: R.1385, E.1386
- Ligands: AMP.25
1 PLIP interactions:1 interactions with chain C- Metal complexes: C:E.1386
MG.40: 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.41: 4 residues within 4Å:- Chain D: L.621, I.622, G.623, 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.42: 6 residues within 4Å:- Chain D: G.1370, E.1390, D.1460
- Ligands: RP5.37, AMP.38, MG.43
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Ligand interactions- Metal complexes: D:G.1370, D:E.1390, D:D.1460, AMP.38
MG.43: 6 residues within 4Å:- Chain D: E.1386, E.1390, D.1459, D.1460
- Ligands: AMP.38, MG.42
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Ligand interactions- Metal complexes: D:E.1386, D:E.1390, D:D.1460, AMP.38, AMP.38
MG.44: 3 residues within 4Å:- Chain D: R.1385, E.1386
- Ligands: AMP.38
1 PLIP interactions:1 interactions with chain D- Metal complexes: D:E.1386
- 12 x CLR: CHOLESTEROL(Non-covalent)
CLR.9: 9 residues within 4Å:- Chain A: I.874, L.878, V.898, I.902, F.905
- Chain D: E.1009, T.1010, M.1013
- Ligands: CLR.36
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain D- Hydrophobic interactions: A:I.874, A:V.898, A:I.902, A:F.905, A:F.905, D:T.1010
CLR.10: 14 residues within 4Å:- Chain A: F.1003, R.1012, P.1015, F.1016, A.1019
- Chain B: V.942, L.945, L.946, L.949, I.972, L.975, F.976, Y.979
- Ligands: CLR.11
12 PLIP interactions:5 interactions with chain B, 7 interactions with chain A- Hydrophobic interactions: B:L.945, B:L.949, B:F.976, B:Y.979, B:Y.979, A:F.1003, A:P.1015, A:F.1016, A:F.1016, A:A.1019
- Hydrogen bonds: A:R.1012, A:R.1012
CLR.11: 6 residues within 4Å:- Chain A: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.10, CLR.21
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.21: 9 residues within 4Å:- Chain A: E.1009, T.1010, M.1013
- Chain B: I.874, L.878, V.898, I.902, F.905
- Ligands: CLR.11
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:I.874, B:V.898, B:I.902, B:F.905, B:F.905, A:T.1010
CLR.22: 14 residues within 4Å:- Chain B: 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.23
12 PLIP interactions:7 interactions with chain B, 5 interactions with chain C- Hydrophobic interactions: B:F.1003, B:P.1015, B:F.1016, B:F.1016, B:A.1019, C:L.945, C:L.949, C:F.976, C:Y.979, C:Y.979
- Hydrogen bonds: B:R.1012, B:R.1012
CLR.23: 6 residues within 4Å:- Chain B: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.22, CLR.32
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.32: 9 residues within 4Å:- Chain B: E.1009, T.1010, M.1013
- Chain C: I.874, L.878, V.898, I.902, F.905
- Ligands: CLR.23
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:I.874, C:V.898, C:I.902, C:F.905, C:F.905, B:T.1010
CLR.33: 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.34
12 PLIP interactions:7 interactions with chain C, 5 interactions with chain D- Hydrophobic interactions: C:F.1003, C:P.1015, C:F.1016, C:F.1016, C:A.1019, D:L.945, D:L.949, D:F.976, D:Y.979, D:Y.979
- Hydrogen bonds: C:R.1012, C:R.1012
CLR.34: 6 residues within 4Å:- Chain C: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.33, CLR.45
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.35: 14 residues within 4Å:- Chain A: 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.36
12 PLIP interactions:7 interactions with chain D, 5 interactions with chain A- Hydrophobic interactions: D:F.1003, D:P.1015, D:F.1016, D:F.1016, D:A.1019, A:L.945, A:L.949, A:F.976, A:Y.979, A:Y.979
- Hydrogen bonds: D:R.1012, D:R.1012
CLR.36: 6 residues within 4Å:- Chain D: E.1009, R.1012, M.1013, F.1016
- Ligands: CLR.9, CLR.35
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.45: 9 residues within 4Å:- Chain C: E.1009, T.1010, M.1013
- Chain D: I.874, L.878, V.898, I.902, F.905
- Ligands: CLR.34
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:I.874, 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
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)
- 4 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Non-covalent)
- 21 x MG: MAGNESIUM ION(Non-covalent)
- 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. To Be Published
- Release Date
- 2024-05-15
- 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.