SMTL ID : 5jvl.1 (1 other biounit)

C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue

Coordinates

PDB Format

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: 16 residues within 4Å: Chain A: K.25, S.93, R.95, T.108, L.110, Q.241, S.242, M.243, V.244, G.279, E.324, T.326, L.335, Q.336, R.338 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.25, A:K.25, A:S.93, A:T.108, A:S.242, A:V.244, A:Q.336, A:Q.336, A:R.338 Salt bridges: A:K.25, A:R.95 6NQ.5: 17 residues within 4Å: Chain B: K.25, S.93, R.95, T.108, L.110, Q.241, S.242, M.243, V.244, G.279, V.283, E.324, T.326, L.335, Q.336, R.338 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.25, B:K.25, B:S.93, B:S.242, B:V.244, B:G.279, B:Q.336, B:R.338 Salt bridges: B:K.25, B:R.95 Halogen bonds: B:T.326

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.324, Q.336 Ligands: 6NQ.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.324 MG.4: 6 residues within 4Å: Chain A: R.619, D.622, R.669, E.748, D.772 Ligands: PEP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.748, A:E.748, A:D.772 MG.6: 3 residues within 4Å: Chain B: E.324, Q.336 Ligands: 6NQ.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.324 MG.8: 5 residues within 4Å: Chain B: R.619, D.622, E.748, D.772 Ligands: PEP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.748, B:D.772, PEP.7

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.3: 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.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.560 Hydrogen bonds: A:N.771, A:N.771, A:D.772 Salt bridges: A:R.562, A:R.619, A:R.782, A:R.782 PEP.7: 14 residues within 4Å: Chain B: H.456, 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.8 10 PLIP interactions: 10 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:H.456, B:R.562, B:R.619, B:R.782, B:R.782

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
D

Pyruvate, phosphate dikinase, chloroplastic

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