SMTL ID : 4av6.1

Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase at 4 A in complex with phosphate and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 12 residues within 4Å: Chain A: D.211, D.241, D.474, D.497, N.501, D.669, K.673 Ligands: PO4.2, MG.3, MG.4, MG.5, MG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.237, A:D.497, A:N.501 Salt bridges: A:K.672, A:K.673 PO4.2: 13 residues within 4Å: Chain A: K.208, D.241, D.245, D.474, N.501, D.669, D.701, K.704, D.705 Ligands: PO4.1, MG.5, MG.6, K.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.245, A:N.501 Salt bridges: A:K.208, A:K.704 PO4.8: 14 residues within 4Å: Chain B: D.211, D.237, D.241, D.474, D.497, N.501, D.669, K.672, K.673 Ligands: PO4.9, MG.10, MG.11, MG.12, MG.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.237, B:D.497, B:N.501 Salt bridges: B:K.672, B:K.673 PO4.9: 13 residues within 4Å: Chain B: K.208, D.241, D.245, D.474, D.497, N.501, D.669, D.701, D.705 Ligands: PO4.8, MG.12, MG.13, K.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.474, B:N.501 Salt bridges: B:K.208, B:K.704

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 6 residues within 4Å: Chain A: D.211, D.215, D.237, D.697 Ligands: PO4.1, MG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.211, A:D.211, A:D.237 MG.4: 5 residues within 4Å: Chain A: D.237, D.241, D.474 Ligands: PO4.1, MG.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.241 MG.5: 9 residues within 4Å: Chain A: K.208, D.211, D.669, D.697, D.701, K.704 Ligands: PO4.1, PO4.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.211, A:D.701, A:D.701 MG.6: 5 residues within 4Å: Chain A: D.241, D.474 Ligands: PO4.1, PO4.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.241, A:D.241, A:D.474 MG.10: 5 residues within 4Å: Chain B: D.211, D.215, D.237, D.697 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.211, B:D.215 MG.11: 1 residues within 4Å: Ligands: PO4.8 No protein-ligand interaction detected (PLIP) MG.12: 8 residues within 4Å: Chain B: K.208, D.211, D.669, D.697, D.701, K.704 Ligands: PO4.8, PO4.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.211, B:D.669, B:D.697, B:D.701, B:D.701 MG.13: 4 residues within 4Å: Chain B: D.241, D.474 Ligands: PO4.8, PO4.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.241, B:D.241

2 x K: POTASSIUM ION(Non-covalent)

K.7: 6 residues within 4Å: Chain A: N.501, A.504, K.508, K.704, D.705 Ligands: PO4.2 No protein-ligand interaction detected (PLIP) K.14: 7 residues within 4Å: Chain B: D.245, N.501, A.504, K.508, K.704, D.705 Ligands: PO4.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kellosalo, J. et al., The Structure and Catalytic Cycle of a Sodium-Pumping Pyrophosphatase. Science (2012)

Release Date

2012-08-08

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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