SMTL ID : 4gnp.1

Structure of rat cytosolic PEPCK Ld_3g in complex with PEP and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: P.285, S.286, A.287, C.288, G.289, K.290, T.291, N.292, G.338, R.436, W.508, F.509, F.517, G.521, F.522, N.525 Ligands: MN.5 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.287, A:C.288, A:G.289, A:K.290, A:T.291, A:N.292, A:N.292, A:G.338, A:R.436, A:F.522, A:N.525 Water bridges: A:P.285, A:K.290, A:K.290, A:T.291, A:T.343, A:N.344, A:R.436, A:W.508, A:W.519, A:W.519 Salt bridges: A:K.290 pi-Stacking: A:F.522, A:F.522 pi-Cation interactions: A:F.517

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

MN.2: 3 residues within 4Å: Chain A: K.244, H.264, D.311 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.264, A:D.311, H2O.2, H2O.2, H2O.3 MN.5: 3 residues within 4Å: Chain A: T.291, D.310 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.291, H2O.22, H2O.22, H2O.22, H2O.22

1 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.3: 11 residues within 4Å: Chain A: A.86, R.87, Y.235, G.236, G.237, K.244, S.286, F.333, N.403, R.405, F.477 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.87, A:G.237, A:S.286, A:N.403, A:N.403 Water bridges: A:R.87, A:R.87, A:R.87, A:R.405, A:R.405, A:R.405, A:R.405, A:R.405, A:R.405 Salt bridges: A:R.87, A:K.244, A:R.405, A:R.405

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

NA.4: 3 residues within 4Å: Chain A: V.65, L.79, N.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65, A:L.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, T.A. et al., The {Omega}-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function. Biochemistry (2012)

Release Date

2013-07-03

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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