SMTL ID : 5jvn.1

C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x 6NQ: 2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid(Non-covalent)

6NQ.1: 12 residues within 4Å: Chain A: K.26, S.94, R.96, T.109, L.111, Q.242, C.243, M.244, V.245, E.325, L.336, Q.337 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.26, A:K.26, A:S.94, A:R.96, A:T.109, A:C.243, A:V.245, A:Q.337 Salt bridges: A:K.26, A:R.96 6NQ.4: 12 residues within 4Å: Chain B: K.26, S.94, R.96, T.109, L.111, Q.242, C.243, M.244, V.245, E.325, L.336, Q.337 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.26, B:K.26, B:S.94, B:R.96, B:C.243, B:V.245, B:Q.337 Salt bridges: B:K.26, B:R.96

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 12 residues within 4Å: Chain A: L.561, R.563, R.620, D.623, R.670, E.749, G.770, T.771, N.772, D.773, G.836 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.561 Hydrogen bonds: A:R.670, A:N.772, A:N.772, A:D.773 Salt bridges: A:R.563, A:R.620 PEP.5: 12 residues within 4Å: Chain B: L.561, R.563, R.620, D.623, R.670, E.749, G.770, T.771, N.772, D.773, G.836 Ligands: MG.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.561 Hydrogen bonds: B:D.623, B:R.670, B:N.772, B:N.772, B:D.773 Salt bridges: B:R.563, B:R.620

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: R.620, D.623, R.670, E.749, D.773 Ligands: PEP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.749, A:D.773 MG.6: 6 residues within 4Å: Chain B: R.620, D.623, R.670, E.749, D.773 Ligands: PEP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.749, B:D.773

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
A

Pyruvate, phosphate dikinase, chloroplastic