SMTL ID : 8b21.1

Time-resolved structure of K+-dependent Na+-PPase from Thermotoga maritima 0-60-seconds post reaction initiation with Na+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 17 residues within 4Å: Chain A: L.559, I.563, Y.622, F.625, I.626, L.629, T.630, V.633, T.634, L.637, L.638, F.642 Chain B: F.427, L.431, V.434, L.435 Ligands: PG4.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.625

13 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: F.439, Y.442 Chain B: F.735 Ligands: PEG.10, PG4.23 No protein-ligand interaction detected (PLIP) PEG.3: 9 residues within 4Å: Chain A: N.547, L.549, D.550 Chain B: Y.275, L.446, F.528, S.541, L.544, L.545 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.547 PEG.10: 10 residues within 4Å: Chain A: L.435, L.438, F.439, Y.442 Chain B: R.552, L.637, L.638, F.735 Ligands: PEG.2, PG4.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.552, B:R.552 PEG.11: 5 residues within 4Å: Chain A: Y.392, K.424, F.427, P.428 Chain B: Y.566 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.566 PEG.12: 7 residues within 4Å: Chain A: K.691, V.694, I.695 Chain B: G.410, T.411, G.412, I.695 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.411 PEG.13: 9 residues within 4Å: Chain A: F.427, L.431 Chain B: L.559, I.563, T.630, V.633, T.634, L.637, L.638 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.630 PEG.14: 4 residues within 4Å: Chain B: Y.391, Y.397, K.398 Ligands: PEG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.398 PEG.15: 7 residues within 4Å: Chain B: F.387, W.388, Y.391, Y.397 Ligands: PG4.9, PEG.14, PG4.21 No protein-ligand interaction detected (PLIP) PEG.16: 9 residues within 4Å: Chain B: L.76, L.77, F.80, T.81, L.632, I.724, A.725, I.728 Ligands: PEG.17 No protein-ligand interaction detected (PLIP) PEG.17: 8 residues within 4Å: Chain B: F.80, L.174, I.176, F.636, I.728, V.732 Ligands: PEG.16, PG4.22 No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain B: K.691, V.694, I.695 No protein-ligand interaction detected (PLIP) PEG.19: 5 residues within 4Å: Chain B: Y.350, F.366, G.367, I.369 Ligands: PEG.20 No protein-ligand interaction detected (PLIP) PEG.20: 5 residues within 4Å: Chain B: F.366, I.369, W.372, F.373 Ligands: PEG.19 No protein-ligand interaction detected (PLIP)

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 12 residues within 4Å: Chain A: I.73, L.76, L.77, F.80, L.190, I.628, L.632, F.636, V.721, I.724, A.725, I.728 No protein-ligand interaction detected (PLIP) PGE.5: 5 residues within 4Å: Chain A: Y.566, Y.570, K.577, Y.622 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) PGE.8: 7 residues within 4Å: Chain A: A.551, R.552, F.735 Chain B: R.365, L.438, D.441, Y.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.438, B:D.441, B:Y.442

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 10 residues within 4Å: Chain A: A.60, T.63, I.66, F.67, A.70, A.93, V.94, A.97, I.101, I.195 No protein-ligand interaction detected (PLIP) PG4.7: 4 residues within 4Å: Chain A: A.28, F.31, A.32, V.102 No protein-ligand interaction detected (PLIP) PG4.9: 12 residues within 4Å: Chain A: I.563, Y.566, Y.622, I.626 Chain B: Y.392, K.424, F.427, P.428 Ligands: LMT.1, PGE.5, PEG.15, PG4.21 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.566, A:Y.566, A:Y.622, A:Y.622, B:K.424 PG4.21: 12 residues within 4Å: Chain B: I.377, S.381, L.384, W.388, F.427, P.428, L.431, T.432, L.435, F.439 Ligands: PG4.9, PEG.15 No protein-ligand interaction detected (PLIP) PG4.22: 6 residues within 4Å: Chain B: H.731, V.732, H.733, L.734 Ligands: PEG.17, PG4.23 No protein-ligand interaction detected (PLIP) PG4.23: 9 residues within 4Å: Chain A: R.365, Y.442 Chain B: R.552, H.733, L.734, F.735 Ligands: PEG.2, PEG.10, PG4.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.552, B:F.735, B:F.735

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strauss, J. et al., Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases. Embo Rep. (2024)

Release Date

2024-01-17

Peptides

K(+)-stimulated pyrophosphate-energized sodium pump: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

K(+)-stimulated pyrophosphate-energized sodium pump

Related Entries With Identical Sequence