SMTL ID : 9ej6.1

Rat cytosolic PEPCK in complex with GTP and beta-sulfopyruvate (313K)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: K.242, H.262, D.309 Ligands: SPV.4, GTP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.262, A:D.309 MN.2: 3 residues within 4Å: Chain A: T.289, D.308 Ligands: GTP.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.289, H2O.1, H2O.1, H2O.1 MN.3: 1 residues within 4Å: Chain A: E.61 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.3

1 x SPV: SULFOPYRUVATE(Non-covalent)

SPV.4: 11 residues within 4Å: Chain A: R.85, G.235, K.241, K.242, H.262, S.284, D.309, F.331, R.403 Ligands: MN.1, GTP.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.235, A:S.284, A:R.403 Water bridges: A:R.85, A:K.241, A:A.465 Salt bridges: A:R.85, A:R.85, A:K.242, A:K.242, A:H.262, A:R.403, A:R.403

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

GTP.5: 23 residues within 4Å: Chain A: H.262, P.283, S.284, A.285, C.286, G.287, K.288, T.289, N.290, D.309, V.333, P.335, R.403, R.434, W.514, F.515, F.523, G.527, F.528, N.531 Ligands: MN.1, MN.2, SPV.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.285, A:C.286, A:G.287, A:K.288, A:T.289, A:T.289, A:N.290, A:V.333, A:R.434, A:F.528, A:N.531 Water bridges: A:G.336, A:R.403, A:R.403, A:W.514, A:P.526 Salt bridges: A:K.288, A:K.288, A:R.403 pi-Stacking: A:F.528, A:F.528 pi-Cation interactions: A:F.523

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]