SMTL ID : 6afz.1

Proton pyrophosphatase-E225H mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 15 residues within 4Å: Chain A: K.250, D.253, D.283, D.287, D.507, N.534, D.691, D.727, K.730, D.731 Ligands: PO4.2, MG.5, MG.6, MG.7, K.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.253 Water bridges: A:K.250, A:K.250, A:K.250, A:K.250, A:D.287, A:N.534, A:K.730, A:K.730 Salt bridges: A:K.250, A:K.730 PO4.2: 11 residues within 4Å: Chain A: D.253, E.268, D.507, D.691, K.694 Ligands: PO4.1, MG.3, MG.4, MG.5, MG.6, MG.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.253, A:E.268 Water bridges: A:K.250, A:K.694, A:K.695, A:K.730 Salt bridges: A:K.250, A:K.694 PO4.15: 15 residues within 4Å: Chain B: K.250, D.253, D.283, D.287, D.507, N.534, D.691, D.727, K.730, D.731 Ligands: PO4.16, MG.19, MG.20, MG.21, K.22 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.283, B:D.691, B:D.731 Water bridges: B:K.250, B:D.287, B:D.287, B:K.730, B:K.730 Salt bridges: B:K.250, B:K.730 PO4.16: 12 residues within 4Å: Chain B: D.253, E.268, D.507, D.691, K.694, D.727 Ligands: PO4.15, MG.17, MG.18, MG.19, MG.20, MG.21 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.507 Water bridges: B:K.250, B:K.250, B:D.253, B:K.694, B:K.730, B:K.730 Salt bridges: B:K.250, B:K.694, B:K.730

10 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.253, D.257, E.268 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.2 MG.4: 4 residues within 4Å: Chain A: D.279, 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.4 MG.5: 8 residues within 4Å: Chain A: K.250, 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: 5 residues within 4Å: Chain A: 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.1 MG.7: 5 residues within 4Å: Chain A: 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.2 MG.17: 5 residues within 4Å: Chain B: D.253, D.257, D.723 Ligands: PO4.16, MG.19 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.253, B:D.257, H2O.6, H2O.6, H2O.7 MG.18: 4 residues within 4Å: Chain B: D.283, D.507 Ligands: PO4.16, MG.20 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.507, H2O.6, H2O.6, H2O.6, H2O.8 MG.19: 7 residues within 4Å: Chain B: K.250, D.253, D.727, K.730 Ligands: PO4.15, PO4.16, MG.17 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.253, B:D.727, H2O.6, H2O.6 MG.20: 5 residues within 4Å: Chain B: D.283, D.507 Ligands: PO4.15, PO4.16, MG.18 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.283, B:D.283, B:D.507, H2O.6, H2O.7 MG.21: 5 residues within 4Å: Chain B: N.534, D.691 Ligands: PO4.15, PO4.16, K.22 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.691, H2O.7

2 x K: POTASSIUM ION(Non-covalent)

K.8: 4 residues within 4Å: Chain A: G.533, N.534 Ligands: PO4.1, MG.7 No protein-ligand interaction detected (PLIP) K.22: 4 residues within 4Å: Chain B: G.533, N.534 Ligands: PO4.15, MG.21 No protein-ligand interaction detected (PLIP)

7 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.9: 2 residues within 4Å: Chain A: L.648, T.652 No protein-ligand interaction detected (PLIP) 1PG.10: 5 residues within 4Å: Chain A: K.397, F.471, T.475 Chain B: L.762, F.763 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.397, A:K.397 1PG.11: 3 residues within 4Å: Chain A: L.762, F.766 Chain B: F.471 No protein-ligand interaction detected (PLIP) 1PG.12: 2 residues within 4Å: Chain A: D.636, K.640 No protein-ligand interaction detected (PLIP) 1PG.13: 4 residues within 4Å: Chain A: I.417, V.421, Y.430, I.468 No protein-ligand interaction detected (PLIP) 1PG.14: 3 residues within 4Å: Chain A: F.141, L.211, I.214 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.211 1PG.23: 4 residues within 4Å: Chain B: M.592, P.644, L.648, T.652 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
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Pyrophosphate-energized vacuolar membrane proton pump