SMTL ID : 2qf2.1 (1 other biounit)

Rat cytosolic PEPCK in complex with oxaloacetic acid and GDP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: K.246, H.266, D.313 Ligands: OAA.6, PYR.9 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.266, A:D.313, H2O.2, PYR.9 MN.2: 4 residues within 4Å: Chain A: T.293 Ligands: MN.3, GDP.7, GDP.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.293, H2O.3 MN.3: 5 residues within 4Å: Chain A: T.293, D.312 Ligands: MN.2, GDP.7, GDP.8 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.293, H2O.3, H2O.6, H2O.9 MN.4: 2 residues within 4Å: Chain A: H.504, E.609 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.504, A:E.609, H2O.12, H2O.16

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

NA.5: 3 residues within 4Å: Chain A: V.67, L.81, N.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.67, A:L.81

1 x OAA: OXALOACETATE ION(Non-covalent)

OAA.6: 13 residues within 4Å: Chain A: R.89, G.239, K.245, K.246, H.266, S.288, D.313, F.335, R.407, A.469, F.487 Ligands: MN.1, PYR.9 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.335 Hydrogen bonds: A:R.89, A:G.239, A:K.245, A:S.288, A:R.407 Water bridges: A:R.89, A:S.288, A:A.289, A:N.405, A:R.407, A:R.407, A:R.407 Salt bridges: A:R.89, A:K.246, A:K.246, A:H.266, A:R.407, A:R.407

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

GDP.7: 19 residues within 4Å: Chain A: P.287, A.289, C.290, G.291, K.292, T.293, N.294, V.337, P.339, G.340, W.518, F.519, F.527, G.531, F.532, N.535 Ligands: MN.2, MN.3, GDP.8 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:K.292, A:K.292, A:V.337, A:R.407, A:W.518, A:W.529, A:P.530, A:P.530 Salt bridges: A:K.292 pi-Stacking: A:F.532 pi-Cation interactions: A:F.527 GDP.8: 20 residues within 4Å: Chain A: P.287, S.288, A.289, C.290, G.291, K.292, T.293, N.294, V.337, G.340, R.438, W.518, F.519, F.527, G.531, F.532, N.535 Ligands: MN.2, MN.3, GDP.7 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:C.290, A:G.291, A:K.292, A:T.293, A:N.294, A:N.294, A:R.438, A:W.518, A:F.532, A:N.535 Water bridges: A:V.337, A:G.340, A:W.518, A:W.529, A:P.530, A:P.530 Salt bridges: A:K.292 pi-Stacking: A:F.532, A:F.532 pi-Cation interactions: A:F.527

1 x PYR: PYRUVIC ACID(Non-covalent)

PYR.9: 10 residues within 4Å: Chain A: R.89, K.245, K.246, H.266, S.288, D.313, R.407, A.469 Ligands: MN.1, OAA.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.288, A:R.407 Water bridges: A:K.245, A:A.289, A:R.407, A:R.407, A:A.469 Salt bridges: A:R.89, A:K.246, A:H.266, A:R.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sullivan, S.M. et al., Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid. Biochemistry (2007)

Release Date

2007-08-28

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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