SMTL ID : 2fah.4 (3 other biounits)

The structure of mitochondrial PEPCK, Complex with Mn and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x TQY- FRU: beta-D-fructofuranose-(2-1)-6-O-octanoyl-alpha-D-glucopyranose(Non-covalent)

TQY-FRU.1: 6 residues within 4Å: Chain A: F.434, R.437, P.538, W.543, E.597, R.604 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.437, A:R.604 Water bridges: A:H.438, A:E.597, A:G.600, A:R.604 Hydrophobic interactions: A:F.434, A:F.434, A:P.538, A:W.543

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

GDP.2: 19 residues within 4Å: Chain A: P.271, S.272, A.273, C.274, G.275, K.276, T.277, N.278, V.321, P.323, G.324, R.422, W.502, F.503, F.511, G.515, F.516, N.519 Ligands: MN.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.273, A:C.274, A:G.275, A:K.276, A:T.277, A:N.278, A:V.321, A:P.323, A:R.422, A:F.516, A:N.519 Water bridges: A:K.276, A:K.276, A:T.277, A:T.277, A:T.329, A:R.391, A:P.514 Salt bridges: A:K.276 pi-Stacking: A:F.516, A:F.516

1 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 8 residues within 4Å: Chain A: R.72, G.223, K.230, S.272, F.319, R.391, A.453 Ligands: MN.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.223, A:S.272, A:A.453 Water bridges: A:R.391, A:R.391, A:R.391, A:R.391 Salt bridges: A:R.72, A:R.72, A:K.230, A:K.230, A:R.391, A:R.391

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

MN.4: 6 residues within 4Å: Chain A: K.230, H.250, S.272, K.276, D.297 Ligands: MLA.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.250, A:D.297, H2O.8 MN.5: 5 residues within 4Å: Chain A: T.277, G.320, V.321, R.391 Ligands: GDP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holyoak, T. et al., Structural Insights into the Mechanism of PEPCK Catalysis. Biochemistry (2006)

Release Date

2006-06-27

Peptides

Phosphoenolpyruvate carboxykinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Phosphoenolpyruvate carboxykinase

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