SMTL ID : 4gmw.1

Structure of rat cytosolic PEPCK Ld_1g in complex with PEP and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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, R.436, W.506, F.507, F.515, W.517, P.518, G.519, F.520, N.523 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.287, A:C.288, A:G.289, A:K.290, A:T.291, A:T.291, A:T.291, A:N.292, A:R.436, A:W.517, A:F.520, A:N.523 Water bridges: A:F.284, A:P.285 pi-Stacking: A:F.507, A:F.507, A:F.515, A:F.520, A:F.520 pi-Cation interactions: A:F.515

4 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.1, H2O.1, H2O.1 MN.5: 2 residues within 4Å: Chain A: H.492, E.597 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.492, A:E.597, H2O.4, H2O.15, H2O.15 MN.6: 3 residues within 4Å: Chain A: K.290, D.310 Ligands: MN.7 No protein-ligand interaction detected (PLIP) MN.7: 3 residues within 4Å: Chain A: D.310, G.334 Ligands: MN.6 No protein-ligand interaction detected (PLIP)

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

NA.3: 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:N.208

1 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.4: 10 residues within 4Å: Chain A: A.86, R.87, Y.235, G.236, G.237, K.244, F.333, N.403, R.405, F.475 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.87, A:G.237, A:N.403, A:N.403 Water bridges: A:R.87, A:K.244, 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

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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