SMTL ID : 3moe.1

The structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 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, SPV.5 28 PLIP interactions: 28 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:W.518, A:F.532, A:N.535 Water bridges: A:A.289, A:N.294, A:N.294, A:V.337, A:V.337, A:G.340, 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, SPV.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.3, H2O.4, H2O.4

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

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

1 x SPV: SULFOPYRUVATE(Non-covalent)

SPV.5: 13 residues within 4Å: Chain A: R.89, G.238, G.239, K.245, K.246, H.266, S.288, D.313, F.335, R.407, F.487 Ligands: GTP.1, MN.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.239, A:S.288, A:R.407 Water bridges: A:R.89, A:R.89, A:R.89, A:K.245, A:S.288, A:R.407 Salt bridges: A:R.89, A:R.89, A:K.246, A:K.246, A:H.266, A:R.407, A:R.407

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

1PE.6: 6 residues within 4Å: Chain A: N.9, G.10, D.12, F.13, A.15, K.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.16 1PE.7: 7 residues within 4Å: Chain A: A.449, S.451, W.452, L.510, P.511, K.512, I.513 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.513 Water bridges: A:L.510 1PE.8: 3 residues within 4Å: Chain A: N.129, A.130, P.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129

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

EDO.9: 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.10: 5 residues within 4Å: Chain A: K.157, I.158, E.190, F.191, I.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.156, A:I.158, A:I.158, A:I.192 EDO.11: 5 residues within 4Å: Chain A: S.413, Q.414, C.415, P.416, I.418 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: R.439, P.440, A.441, I.477, F.586 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.439, A:A.441, A:R.463 Water bridges: A:R.463, A:E.590

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
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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