- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 10 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 5 residues within 4Å:- Chain A: D.253, D.257, D.723
- Ligands: PO4.2, MG.5
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:D.253, A:D.257, H2O.1, H2O.1, H2O.1
MG.4: 4 residues within 4Å:- Chain A: D.269, D.507
- Ligands: PO4.2, MG.6
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.507, H2O.1, H2O.1, H2O.2, H2O.6
MG.5: 7 residues within 4Å:- Chain A: D.253, D.723, D.727, K.730
- Ligands: PO4.1, PO4.2, MG.3
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.253, A:D.727, H2O.1, H2O.1
MG.6: 6 residues within 4Å:- Chain A: D.279, D.283, D.507
- Ligands: PO4.1, PO4.2, MG.4
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.283, A:D.507, H2O.1, H2O.3
MG.7: 6 residues within 4Å:- Chain A: D.530, N.534, D.691
- Ligands: PO4.1, PO4.2, K.8
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.691, H2O.1, H2O.1
MG.15: 4 residues within 4Å:- Chain B: D.253, D.257
- Ligands: PO4.14, MG.17
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.253, B:D.257, H2O.8, H2O.8, H2O.11
MG.16: 4 residues within 4Å:- Chain B: D.283, D.507
- Ligands: PO4.14, MG.18
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.507, H2O.8, H2O.9, H2O.10, H2O.11
MG.17: 7 residues within 4Å:- Chain B: K.250, D.253, D.727, K.730
- Ligands: PO4.13, PO4.14, MG.15
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.253, B:D.727, H2O.8, H2O.8
MG.18: 5 residues within 4Å:- Chain B: D.283, D.507
- Ligands: PO4.13, PO4.14, MG.16
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.283, B:D.283, B:D.507, H2O.8, H2O.11
MG.19: 5 residues within 4Å:- Chain B: N.534, D.691
- Ligands: PO4.13, PO4.14, K.20
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.691, H2O.8, H2O.9
- 2 x K: POTASSIUM ION(Non-covalent)
- 6 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)
1PG.9: 3 residues within 4Å:- Chain A: M.592, L.651, T.652
No protein-ligand interaction detected (PLIP)1PG.10: 5 residues within 4Å:- Chain A: F.660, L.762, F.763, F.766
- Chain B: F.471
No protein-ligand interaction detected (PLIP)1PG.11: 2 residues within 4Å:- Chain A: D.636, I.643
No protein-ligand interaction detected (PLIP)1PG.12: 4 residues within 4Å:- Chain A: I.417, F.420, V.421, Y.430
No protein-ligand interaction detected (PLIP)1PG.21: 4 residues within 4Å:- Chain B: M.592, P.644, L.648, T.652
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.652
1PG.22: 6 residues within 4Å:- Chain A: F.471, T.475
- Chain B: F.660, L.762, F.763, F.766
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tsai, J.Y. et al., Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. (2019)
- Release Date
- 2019-04-10
- Peptides
- Pyrophosphate-energized vacuolar membrane proton pump: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 10 x MG: MAGNESIUM ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 6 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tsai, J.Y. et al., Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation. J. Mol. Biol. (2019)
- Release Date
- 2019-04-10
- Peptides
- Pyrophosphate-energized vacuolar membrane proton pump: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B - Membrane
-
We predict this structure to be a membrane protein.