SMTL ID : 6afv.1

Proton pyrophosphatase-L555K mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.253, A:D.731 Water bridges: A:D.287, A:D.287, A:N.534, A:K.730, A:K.730 Salt bridges: A:K.250, A:K.730 PO4.2: 12 residues within 4Å: Chain A: D.253, D.257, D.507, D.530, D.691, K.694 Ligands: PO4.1, MG.3, MG.4, MG.5, MG.6, MG.7 7 PLIP interactions: 7 interactions with chain A Water bridges: A:E.268, A:E.268, A:K.694, A:K.694, A:K.694, A:D.723 Salt bridges: A:K.694 PO4.12: 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: PO4.13, MG.16, MG.17, MG.18, K.19 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.283, B:D.727 Water bridges: B:D.287, B:D.727, B:K.730 Salt bridges: B:K.250, B:K.730 PO4.13: 12 residues within 4Å: Chain B: D.253, E.268, D.507, D.530, D.691, D.727 Ligands: PO4.12, MG.14, MG.15, MG.16, MG.17, MG.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.268, B:D.727 Water bridges: B:K.730 Salt bridges: B:K.694

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: 3 residues within 4Å: Chain A: 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.2, H2O.2, H2O.3 MG.5: 7 residues within 4Å: Chain A: K.250, D.253, 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: 8 residues within 4Å: Chain A: K.250, D.253, D.279, D.283, D.507 Ligands: PO4.1, PO4.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.283, A:D.507, H2O.1 MG.7: 6 residues within 4Å: Chain A: D.530, N.534, D.691 Ligands: PO4.1, PO4.2, K.8 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain B: D.253, D.257 Ligands: PO4.13, MG.16 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.15: 4 residues within 4Å: Chain B: D.279, D.507 Ligands: PO4.13, MG.17 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.16: 6 residues within 4Å: Chain B: D.253, D.727, K.730 Ligands: PO4.12, PO4.13, MG.14 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.17: 7 residues within 4Å: Chain B: K.250, D.253, D.283, D.507 Ligands: PO4.12, PO4.13, MG.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.283, B:D.507, H2O.6 MG.18: 6 residues within 4Å: Chain B: D.530, N.534, D.691 Ligands: PO4.12, PO4.13, K.19 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain A: G.533, N.534, A.537 Ligands: PO4.1, MG.7 No protein-ligand interaction detected (PLIP) K.19: 3 residues within 4Å: Chain B: N.534 Ligands: PO4.12, MG.18 No protein-ligand interaction detected (PLIP)

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

1PG.9: 7 residues within 4Å: Chain A: V.581, M.592, L.648, L.651, T.652, V.655, V.656 No protein-ligand interaction detected (PLIP) 1PG.10: 6 residues within 4Å: Chain A: I.577, L.762, F.766 Chain B: I.468, F.471 Ligands: 1PG.22 No protein-ligand interaction detected (PLIP) 1PG.11: 3 residues within 4Å: Chain A: D.636, K.640, I.643 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.636 1PG.20: 5 residues within 4Å: Chain A: K.457 Chain B: W.588, M.592, L.648, T.652 No protein-ligand interaction detected (PLIP) 1PG.21: 7 residues within 4Å: Chain A: F.471, T.475 Chain B: I.577, F.660, L.762, F.763, F.766 No protein-ligand interaction detected (PLIP) 1PG.22: 6 residues within 4Å: Chain B: Y.424, K.457, I.460, F.464, I.468 Ligands: 1PG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.457

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