SMTL ID : 5lu4.2 (1 other biounit)

C4-type pyruvate phosphate dikinase: conformational intermediate of central domain in the swiveling mechanism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 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.280, E.324, L.335, Q.336 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.93, A:T.108, A:S.242, A:V.244, A:G.279, A:E.324 Salt bridges: A:K.25, A:K.25, A:R.95 ADP.4: 15 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, E.280, E.324, L.335, Q.336 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.93, B:T.108, B:S.242, B:V.244, B:G.279, B:E.280, B:Q.336 Salt bridges: B:K.25, B:K.25, B:R.95

4 x MG: MAGNESIUM ION(Non-covalent)

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

1 x PYR: PYRUVIC ACID(Non-covalent)

PYR.6: 8 residues within 4Å: Chain B: L.560, R.619, E.748, G.769, T.770, N.771, D.772 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.560 Hydrogen bonds: B:N.771, B:N.771, B:D.772

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minges, A. et al., Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism. Protein Sci. (2017)

Release Date

2017-05-24

Peptides

Pyruvate, phosphate dikinase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Pyruvate, phosphate dikinase, chloroplastic

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