SMTL ID : 4a01.1

Crystal Structure of the H-Translocating Pyrophosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.253, D.257, D.723 Ligands: MG.3, 2PN.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.253, A:D.257, H2O.5, H2O.5, H2O.5 MG.2: 4 residues within 4Å: Chain A: D.269, D.507 Ligands: MG.4, 2PN.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.507, H2O.5, H2O.5, H2O.5, H2O.6 MG.3: 5 residues within 4Å: Chain A: D.253, D.727, K.730 Ligands: MG.1, 2PN.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.253, A:D.727, H2O.5, H2O.12 MG.4: 4 residues within 4Å: Chain A: D.283, D.507 Ligands: MG.2, 2PN.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.283, A:D.507, H2O.5, H2O.6 MG.5: 4 residues within 4Å: Chain A: N.534, D.691 Ligands: K.6, 2PN.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.691, H2O.9, H2O.9 MG.13: 5 residues within 4Å: Chain B: D.253, D.257, D.723 Ligands: MG.15, 2PN.19 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.253, B:D.257, H2O.16, H2O.16, H2O.16 MG.14: 5 residues within 4Å: Chain B: D.269, D.279, D.507 Ligands: MG.16, 2PN.19 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.507, H2O.17, H2O.17, H2O.17, H2O.17 MG.15: 6 residues within 4Å: Chain B: K.250, D.253, D.727, K.730 Ligands: MG.13, 2PN.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.253, B:D.727, H2O.16, H2O.22 MG.16: 4 residues within 4Å: Chain B: D.283, D.507 Ligands: MG.14, 2PN.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.283, B:D.507, H2O.16, H2O.17 MG.17: 4 residues within 4Å: Chain B: N.534, D.691 Ligands: K.18, 2PN.19 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.691, H2O.20, H2O.20

2 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: G.533, N.534 Ligands: MG.5, 2PN.7 No protein-ligand interaction detected (PLIP) K.18: 3 residues within 4Å: Chain B: N.534 Ligands: MG.17, 2PN.19 No protein-ligand interaction detected (PLIP)

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.7: 18 residues within 4Å: Chain A: K.250, D.253, E.268, D.283, D.287, D.507, N.534, D.691, K.694, D.727, K.730, D.731 Ligands: MG.1, MG.2, MG.3, MG.4, MG.5, K.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.250, A:K.694, A:K.730 Water bridges: A:D.253, A:N.280, A:D.287, A:D.287, A:D.287, A:N.534, A:D.691, A:K.695, A:D.723, A:D.723, A:K.730, A:D.731 2PN.19: 18 residues within 4Å: Chain B: K.250, D.253, E.268, D.283, D.287, D.507, N.534, D.691, K.694, D.727, K.730, D.731 Ligands: MG.13, MG.14, MG.15, MG.16, MG.17, K.18 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.250, B:D.287, B:D.287, B:D.507, B:K.694, B:D.727, B:K.730 Water bridges: B:D.287, B:D.287, B:K.695

9 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.8: 7 residues within 4Å: Chain A: K.362, F.420, Y.424, Y.430, F.464, A.465, I.468 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.464, A:I.468 Hydrogen bonds: A:K.362 DMU.9: 6 residues within 4Å: Chain A: W.588, M.592, L.648, T.652 Chain B: K.457 Ligands: DMU.23 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.457 Hydrophobic interactions: A:W.588 Water bridges: A:E.641, A:E.641 DMU.10: 7 residues within 4Å: Chain A: Y.95, F.99, D.636, I.639, K.640, I.643, A.647 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.99, A:F.99, A:I.643 Hydrogen bonds: A:Y.95, A:D.636, A:D.636 DMU.11: 6 residues within 4Å: Chain A: I.577, F.660, L.762, F.763 Chain B: F.471 Ligands: DMU.23 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.577, A:F.660, A:F.763, B:F.471, B:F.471 DMU.12: 4 residues within 4Å: Chain A: F.110, S.113, G.116, H.758 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.110 DMU.20: 8 residues within 4Å: Chain A: K.457 Chain B: W.588, K.640, E.641, P.644, L.648, T.652, V.656 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.457, A:K.457, B:K.640, B:K.640, B:E.641 Water bridges: A:K.457 Hydrophobic interactions: B:L.648, B:V.656 DMU.21: 3 residues within 4Å: Chain B: S.401, W.402, F.405 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.402, B:F.405, B:F.405 DMU.22: 6 residues within 4Å: Chain A: F.471, T.475 Chain B: I.577, F.660, F.763, F.766 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.577, B:F.660, B:F.763, B:F.763, A:F.471 Water bridges: A:K.397, A:K.397, A:T.475 DMU.23: 10 residues within 4Å: Chain A: W.588 Chain B: Y.424, Y.425, K.457, I.460, I.461, F.464, I.468 Ligands: DMU.9, DMU.11 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.464, B:I.468 Hydrogen bonds: B:Y.424, B:Y.424, B:Y.425, B:K.457, A:W.588 Water bridges: B:Y.425 Salt bridges: B:K.457

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, S.-M. et al., Crystal Structure of a Membrane Embedded H1-Translocating Pyrophosphatase. Nature (2012)

Release Date

2012-03-28

Peptides

PROTON PYROPHOSPHATASE: 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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PROTON PYROPHOSPHATASE

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