SMTL ID : 9eiv.1

Rat cytosolic PEPCK in complex with GDP and phosphoglycolic acid (253K)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: K.244, H.264, D.311 Ligands: PGA.4 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.2: 4 residues within 4Å: Chain A: T.291, D.310 Ligands: PGA.4, GDP.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.291, H2O.1, H2O.1 MN.3: 2 residues within 4Å: Chain A: H.502, E.607 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.502, A:E.607, A:E.607

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

PGA.4: 12 residues within 4Å: Chain A: R.87, K.244, H.264, S.286, A.287, K.290, D.311, R.405, F.485 Ligands: MN.1, MN.2, GDP.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.286, A:A.287 Water bridges: A:R.87, A:R.87, A:K.290, A:V.335, A:R.405, A:R.405 Salt bridges: A:R.87, A:K.244, A:K.244, A:H.264, A:K.290, A:R.405, A:R.405

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

GDP.5: 18 residues within 4Å: Chain A: P.285, A.287, C.288, G.289, K.290, T.291, N.292, P.337, G.338, R.436, W.516, F.517, F.525, G.529, F.530, N.533 Ligands: MN.2, PGA.4 21 PLIP interactions: 21 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:P.337, A:G.338, A:F.530, A:N.533 Water bridges: A:S.286, A:K.290, A:T.291, A:T.291, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McLeod, M.J. et al., A structural perspective on the temperature dependent activity of enzymes. Structure (2025)

Release Date

2025-04-09

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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