SMTL ID : 4gnm.1

Structure of rat cytosolic PEPCK Ld_2g in complex with oxalate and GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: H.264, P.285, S.286, A.287, C.288, G.289, K.290, T.291, N.292, D.311, V.335, R.405, R.436, W.507, F.508, F.516, G.520, F.521, N.524 Ligands: MN.2, MN.3, OXL.6 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:A.287, A:C.288, A:G.289, A:K.290, A:T.291, A:R.436, A:F.521, A:N.524 Water bridges: A:R.87, A:A.287, A:N.292, A:N.292, A:V.335, A:G.338, A:T.343, A:N.403, A:R.405, A:W.507, A:W.518, A:W.518, A:P.519 Salt bridges: A:K.290, A:K.290, A:R.405 pi-Stacking: A:F.521, A:F.521 pi-Cation interactions: A:F.516

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

MN.2: 5 residues within 4Å: Chain A: K.244, H.264, D.311 Ligands: GTP.1, OXL.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.264, A:D.311 MN.3: 3 residues within 4Å: Chain A: T.291, D.310 Ligands: GTP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.291, H2O.1, H2O.2, H2O.3

2 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:L.79, A:L.79 NA.5: 2 residues within 4Å: Chain A: H.493, E.598 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.598

1 x OXL: OXALATE ION(Non-covalent)

OXL.6: 11 residues within 4Å: Chain A: R.87, K.243, K.244, H.264, S.286, D.311, F.333, R.405, F.476 Ligands: GTP.1, MN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.286 Water bridges: A:R.87, A:K.243, A:K.243 Salt bridges: A:R.87, A:K.243, A:K.244, A:K.244, A:H.264, A:R.405, A:R.405

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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