SMTL ID : 5lzq.1

Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.211, D.215, D.697, D.701 Ligands: MG.3, 2PN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.211, A:D.211, A:D.215 MG.2: 6 residues within 4Å: Chain A: E.226, D.227, D.237, D.474 Ligands: MG.4, 2PN.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.474, A:D.474 MG.3: 6 residues within 4Å: Chain A: K.208, D.211, D.697, D.701 Ligands: MG.1, 2PN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.211, A:D.701, A:D.701 MG.4: 5 residues within 4Å: Chain A: D.237, D.241, D.474 Ligands: MG.2, 2PN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.241, A:D.241, A:D.474 MG.5: 4 residues within 4Å: Chain A: D.497, N.501, D.669 Ligands: 2PN.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.669 MG.10: 6 residues within 4Å: Chain B: K.208, D.211, D.697, D.701 Ligands: MG.14, 2PN.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.211, B:D.701, B:D.701 MG.11: 6 residues within 4Å: Chain B: E.226, D.227, D.237, D.474 Ligands: MG.12, 2PN.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.237 MG.12: 5 residues within 4Å: Chain B: D.237, D.241, D.474 Ligands: MG.11, 2PN.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.237, B:D.241, B:D.241, B:D.474 MG.13: 4 residues within 4Å: Chain B: D.497, N.501, D.669 Ligands: 2PN.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.669 MG.14: 6 residues within 4Å: Chain B: D.211, D.215, D.697, D.701 Ligands: MG.10, 2PN.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.211, B:D.211, B:D.215

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

2PN.6: 18 residues within 4Å: Chain A: K.208, D.211, D.215, E.226, D.241, D.245, D.474, D.497, N.501, D.669, D.697, D.701, K.704 Ligands: MG.1, MG.2, MG.3, MG.4, MG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.474, A:K.704, A:D.705 2PN.8: 3 residues within 4Å: Chain A: K.278, E.281, S.534 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.278, A:E.281 2PN.9: 4 residues within 4Å: Chain A: M.527, L.542, V.543, L.545 No protein-ligand interaction detected (PLIP) 2PN.15: 18 residues within 4Å: Chain B: K.208, D.211, D.215, E.226, D.241, D.245, D.474, D.497, N.501, D.669, K.672, D.701, K.704 Ligands: MG.10, MG.11, MG.12, MG.13, MG.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.208, B:K.208, B:D.669, B:K.672, B:K.704, B:K.704

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: D.252, E.255, S.256, D.712, I.713, K.716 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.252, A:D.712, A:K.716 NA.16: 6 residues within 4Å: Chain B: D.252, E.255, S.256, D.712, I.713, K.716 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.252, B:D.252, B:K.716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, K.M. et al., Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism. Nat Commun (2016)

Release Date

2016-12-14

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.
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K(+)-stimulated pyrophosphate-energized sodium pump

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