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

PYRUVATE PHOSPHATE DIKINASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 5 residues within 4Å: Chain A: D.619, L.706, E.744, D.768 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.744 Water bridges: A:R.616 NH4.7: 5 residues within 4Å: Chain B: D.619, L.706, E.744, D.768 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.619 Water bridges: B:R.616, B:E.744

10 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:M.98, A:G.100, A:M.101, A:M.102 Water bridges: A:M.102, A:T.104, A:T.104, A:Q.334, A:Q.334, A:R.336, A:R.336 Salt bridges: A:K.21, A:R.336 SO4.3: 5 residues within 4Å: Chain A: K.717, E.757, E.758, E.760, R.822 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.822, A:R.822, A:R.822 Salt bridges: A:K.717, A:R.822 SO4.4: 5 residues within 4Å: Chain A: R.522, W.526 Chain B: R.522, W.526 Ligands: SO4.10 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Water bridges: B:E.360, B:E.360, B:W.526, A:E.360, A:E.360, A:W.526 Salt bridges: B:R.522, A:R.522 SO4.5: 4 residues within 4Å: Chain A: R.616, N.767, D.768 Ligands: NH4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.767, A:D.768 Water bridges: A:R.616, A:R.616, A:D.768 Salt bridges: A:R.616 SO4.6: 3 residues within 4Å: Chain A: P.659, M.660, R.664 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.664, A:R.664, A:R.664, A:D.779 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 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:M.98, B:G.100, B:M.101, B:M.102 Water bridges: B:R.91, B:M.102, B:T.104, B:T.104, B:Q.334, B:Q.334, B:R.336 Salt bridges: B:K.21, B:R.336 SO4.9: 5 residues within 4Å: Chain B: K.717, E.757, E.758, E.760, R.822 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.822, B:R.822, B:R.822 Salt bridges: B:K.717, B:R.822 SO4.10: 5 residues within 4Å: Chain A: R.522, W.526 Chain B: R.522, W.526 Ligands: SO4.4 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Water bridges: B:E.360, B:E.360, B:W.526, A:E.360, A:W.526 Salt bridges: B:R.522, A:R.522 SO4.11: 4 residues within 4Å: Chain B: R.616, N.767, D.768 Ligands: NH4.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.767, B:D.768 Water bridges: B:R.616, B:R.616, B:E.744, B:D.768 Salt bridges: B:R.616 SO4.12: 3 residues within 4Å: Chain B: P.659, M.660, R.664 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.664, B:R.664, B:R.664 Salt bridges: B:R.664

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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