SMTL ID : 5v9g.1

Structure of the H477R variant of rat cytosolic PEPCK in complex with oxalate and GTP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

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

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

GTP.3: 24 residues within 4Å: Chain A: H.264, P.285, S.286, A.287, C.288, G.289, K.290, T.291, N.292, D.311, V.335, P.337, G.338, R.405, R.436, W.516, F.517, F.525, G.529, F.530, N.533 Ligands: MN.1, MN.2, OXL.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:V.335, A:G.338, A:R.436, A:F.530, A:N.533 Water bridges: A:R.405, A:R.405, A:R.436, A:W.516, A:P.528 Salt bridges: A:K.290, A:K.290, A:R.405 pi-Stacking: A:F.530 pi-Cation interactions: A:F.525

1 x OXL: OXALATE ION(Non-covalent)

OXL.4: 11 residues within 4Å: Chain A: R.87, Y.235, K.244, H.264, S.286, D.311, F.333, R.405, A.467 Ligands: MN.1, GTP.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.235, A:S.286 Water bridges: A:K.243, A:K.243, A:R.405, A:R.405 Salt bridges: A:R.87, A:K.243, A:K.244, A:K.244, A:H.264, 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:L.79, A:N.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, D.S. et al., Asymmetric Anchoring Is Required for Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase. Biochemistry (2017)

Release Date

2017-04-12

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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