SMTL ID : 1kc7.1 (1 other biounit)

Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.744, D.768 Ligands: PPR.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.744, A:D.768 MG.7: 3 residues within 4Å: Chain B: E.744, D.768 Ligands: PPR.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.744, B:D.768

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: K.21, M.98, P.99, G.100, M.101, M.102, R.336 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.100, A:M.101, A:M.102 Salt bridges: A:K.21, A:R.336 SO4.3: 6 residues within 4Å: Chain A: R.522, W.526 Chain B: E.360, R.522, W.526 Ligands: SO4.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.360 Salt bridges: B:R.522, A:R.522 SO4.4: 4 residues within 4Å: Chain A: K.717, E.757, E.758, R.822 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.717, A:R.822 SO4.5: 3 residues within 4Å: Chain A: P.659, M.660, R.664 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.664 SO4.8: 7 residues within 4Å: Chain B: K.21, M.98, P.99, G.100, M.101, M.102, R.336 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.100, B:M.101, B:M.102 Salt bridges: B:K.21, B:R.336 SO4.9: 6 residues within 4Å: Chain A: E.360, R.522, W.526 Chain B: R.522, W.526 Ligands: SO4.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.522, B:R.522 SO4.10: 4 residues within 4Å: Chain B: K.717, E.757, E.758, R.822 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.717, B:R.822 SO4.11: 3 residues within 4Å: Chain B: P.659, M.660, R.664 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.664

2 x PPR: PHOSPHONOPYRUVATE(Non-covalent)

PPR.6: 12 residues within 4Å: Chain A: L.558, R.560, R.616, M.742, E.744, G.765, T.766, N.767, D.768, C.830, G.831 Ligands: MG.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.560, A:R.560, A:R.616, A:R.616, A:N.767, A:N.767, A:D.768 PPR.12: 12 residues within 4Å: Chain B: L.558, R.560, R.616, M.742, E.744, G.765, T.766, N.767, D.768, C.830, G.831 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.560, B:R.560, B:R.616, B:R.616, B:N.767, B:N.767, B:D.768

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herzberg, O. et al., Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis. Biochemistry (2002)

Release Date

2002-01-30

Peptides

pyruvate phosphate dikinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

pyruvate phosphate dikinase

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