SMTL ID : 3dtb.2 (2 other biounits)

The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.1: 10 residues within 4Å: Chain A: R.89, G.238, G.239, K.245, K.246, S.288, D.313, F.335, R.407 Ligands: MN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.239 Water bridges: A:R.89, A:R.89, A:R.89, A:K.245, A:K.245, A:R.407, A:R.407 Salt bridges: A:R.89, A:R.89, A:K.245, A:K.246, A:R.407, A:R.407

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: K.246, H.266, D.313 Ligands: PGA.1 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:H.266, A:D.313, PGA.1, H2O.19, H2O.27 MN.3: 3 residues within 4Å: Chain A: T.293, D.312 Ligands: GDP.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.293, H2O.2, H2O.2, H2O.3, H2O.19

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: L.81, N.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.67, A:L.81

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.5: 17 residues within 4Å: Chain A: P.287, S.288, A.289, C.290, G.291, K.292, T.293, N.294, G.340, R.438, W.518, F.519, F.527, G.531, F.532, N.535 Ligands: MN.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.289, A:C.290, A:G.291, A:K.292, A:T.293, A:N.294, A:N.294, A:G.340, A:R.438, A:F.532, A:N.535 Water bridges: A:P.287, A:T.293, A:V.337, A:V.337, A:T.345, A:R.438, A:W.529, A:P.530, A:P.530 pi-Stacking: A:F.532, A:F.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sullivan, S.M. et al., Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-08-26

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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