SMTL ID : 3dt2.1

The structure of rat cytosolic PEPCK in complex with oxalate and GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: T.293, D.312 Ligands: GTP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.293, H2O.4, H2O.4, H2O.6 MN.2: 5 residues within 4Å: Chain A: K.246, H.266, D.313 Ligands: OXL.3, GTP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.266, A:D.313

1 x OXL: OXALATE ION(Non-covalent)

OXL.3: 10 residues within 4Å: Chain A: R.89, K.246, H.266, S.288, D.313, R.407, A.469, F.487 Ligands: MN.2, GTP.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.237, A:S.288 Water bridges: A:R.89, A:K.245, A:R.407, A:A.469 Salt bridges: A:R.89, A:K.245, A:K.246, A:K.246, A:H.266, A:R.407, A:R.407

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 GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 24 residues within 4Å: Chain A: H.266, P.287, S.288, A.289, C.290, G.291, K.292, T.293, N.294, D.313, V.337, P.339, G.340, R.407, R.438, W.518, F.519, F.527, G.531, F.532, N.535 Ligands: MN.1, MN.2, OXL.3 24 PLIP interactions: 24 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:V.337, A:G.340, A:R.438, A:F.532, A:N.535 Water bridges: A:T.345, A:R.407, A:R.407, A:R.438, A:W.529, A:P.530, A:P.530 Salt bridges: A:K.292, A:K.292, A:R.407 pi-Stacking: A:F.532, A:F.532

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 7 residues within 4Å: Chain A: L.155, W.262, W.316, M.317, K.318, R.326, E.426 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.318 Water bridges: A:E.260, A:E.260

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
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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