SMTL ID : 3mof.2 (1 other biounit)

The structure of rat cytosolic PEPCK mutant A467G in complex with oxalate and GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: H.266, P.287, S.288, A.289, C.290, G.291, K.292, T.293, N.294, D.313, V.337, R.407, R.438, W.518, F.519, F.527, G.531, F.532, N.535 Ligands: MN.2, MN.3, OXL.5 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:A.289, A:C.290, A:G.291, A:K.292, A:T.293, A:R.438, A:F.532, A:N.535 Water bridges: A:N.294, A:V.337, A:V.337, A:G.340, A:T.345, A:R.407, A:R.407, A:R.438, A:W.518, A:W.529, A:P.530, A:P.530 Salt bridges: A:K.292, A:K.292, A:R.407 pi-Stacking: A:F.532, A:F.532 pi-Cation interactions: A:F.527

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

MN.2: 6 residues within 4Å: Chain A: K.246, H.266, K.292, D.313 Ligands: GTP.1, OXL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.266, A:D.313 MN.3: 3 residues within 4Å: Chain A: T.293, D.312 Ligands: GTP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.293, H2O.2, H2O.4, H2O.8

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

NA.4: 3 residues within 4Å: Chain A: V.67, L.81, N.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.81, A:L.81

1 x OXL: OXALATE ION(Non-covalent)

OXL.5: 9 residues within 4Å: Chain A: R.89, K.245, K.246, H.266, S.288, D.313, R.407 Ligands: GTP.1, MN.2 10 PLIP interactions: 10 interactions with chain A Water bridges: A:K.245, A:K.245, A:R.407 Salt bridges: A:R.89, A:K.245, A:K.246, A:K.246, A:H.266, A:R.407, A:R.407

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 5 residues within 4Å: Chain A: N.9, G.10, D.12, A.15, K.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.16

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: A.449, S.451, W.452, P.511, K.512, I.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.513, A:I.513 Water bridges: A:K.512, A:K.512 EDO.8: 2 residues within 4Å: Chain A: R.545, Y.559 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.545, A:R.545 Water bridges: A:D.550 EDO.9: 4 residues within 4Å: Chain A: F.32, N.36, K.193, E.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.36, A:K.193, A:E.229 Water bridges: A:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, T.A. et al., Increasing the conformational entropy of the Omega-loop lid domain in phosphoenolpyruvate carboxykinase impairs catalysis and decreases catalytic fidelity . Biochemistry (2010)

Release Date

2010-06-02

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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