SMTL ID : 5jvj.1

C4-type pyruvate phosphate dikinase: different conformational states of the nucleotide binding domain in the dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 13 residues within 4Å: Chain A: L.560, R.562, R.619, M.746, E.748, G.769, T.770, N.771, D.772, R.782, C.834, G.835 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.560 Hydrogen bonds: A:N.771, A:N.771, A:D.772, A:D.772 Salt bridges: A:R.562, A:R.619, A:R.782, A:R.782 PEP.3: 12 residues within 4Å: Chain B: L.560, R.562, R.619, E.748, G.769, T.770, N.771, D.772, R.782, C.834, G.835 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.560 Hydrogen bonds: B:R.669, B:N.771, B:N.771, B:D.772 Salt bridges: B:R.562, B:R.619, B:R.782

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: R.619, D.622, R.669, E.748, D.772 Ligands: PEP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.748, A:E.748, A:D.772, PEP.1 MG.4: 6 residues within 4Å: Chain B: R.619, D.622, R.669, E.748, D.772 Ligands: PEP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.748, B:D.772

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minges, A. et al., Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase. Sci Rep (2017)

Release Date

2017-04-05

Peptides

Pyruvate, phosphate dikinase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyruvate, phosphate dikinase, chloroplastic

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