SMTL ID : 5fh5.1

The structure of rat cytosolic PEPCK variant E89Q in complex with phosphoglycolate and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: T.291, D.310 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.291, H2O.1, H2O.1, H2O.4, H2O.8 MN.2: 4 residues within 4Å: Chain A: K.244, H.264, D.311 Ligands: PGA.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.264, A:D.311, H2O.1, H2O.5

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

GDP.3: 16 residues within 4Å: Chain A: P.285, S.286, A.287, C.288, G.289, K.290, T.291, N.292, R.436, W.516, F.517, F.525, G.529, F.530, N.533 Ligands: MN.1 17 PLIP interactions: 17 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:R.436, A:F.530, A:N.533 Water bridges: A:V.335, A:V.335, A:V.335, A:P.528 Salt bridges: A:K.290 pi-Stacking: A:F.530, A:F.530 pi-Cation interactions: A:F.525

1 x PGA: 2-PHOSPHOGLYCOLIC ACID(Non-covalent)

PGA.4: 10 residues within 4Å: Chain A: R.87, G.236, G.237, K.243, K.244, S.286, D.311, F.333, R.405 Ligands: MN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.237 Water bridges: A:R.87, A:R.87, A:K.243, A:K.243, A:S.286, A:R.405, A:R.405 Salt bridges: A:R.87, A:R.87, A:K.243, A:K.244, A:R.405, A:R.405

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

NA.5: 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., Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Biochemistry (2016)

Release Date

2016-11-09

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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