SMTL ID : 4gnq.1

Structure of rat cytosolic PEPCK Ld_3g in complex with oxalate and GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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.508, F.509, F.517, G.521, F.522, N.525 Ligands: MN.2, MN.3, OXL.5 33 PLIP interactions: 33 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.522, A:N.525 Water bridges: A:S.286, A:S.286, A:A.287, A:T.291, A:N.292, A:N.292, A:V.335, A:V.335, A:V.335, A:G.338, A:T.343, A:R.405, A:R.405, A:R.436, A:W.508, A:W.519, A:W.519, A:P.520 Salt bridges: A:K.244, A:K.290, A:K.290, A:R.405 pi-Stacking: A:F.522, A:F.522 pi-Cation interactions: A:F.517

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.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.264, A:D.311, H2O.27 MN.3: 3 residues within 4Å: Chain A: T.291, D.310 Ligands: GTP.1 No protein-ligand interaction detected (PLIP)

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

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

1 x OXL: OXALATE ION(Non-covalent)

OXL.5: 11 residues within 4Å: Chain A: R.87, K.243, K.244, H.264, S.286, D.311, F.333, R.405, F.477 Ligands: GTP.1, MN.2 13 PLIP interactions: 13 interactions with chain A Water bridges: A:R.87, A:R.87, A:K.243, A:K.243, A:S.286, A:N.403 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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