SMTL ID : 5v9h.1 (1 other biounit)

Structure of the H477R variant of rat cytosolic PEPCK in complex with phosphoglycolate and GDP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

1PE.1: 5 residues within 4Å: Chain A: L.153, W.260, K.316, R.324, E.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.316 Water bridges: A:K.316

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

MN.2: 4 residues within 4Å: Chain A: T.291, D.310 Ligands: GDP.6, PGA.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.291, H2O.1, H2O.1, H2O.1 MN.3: 2 residues within 4Å: Chain A: H.502, E.607 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.502, A:E.607, A:E.607, H2O.3 MN.4: 4 residues within 4Å: Chain A: K.244, H.264, D.311 Ligands: PGA.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.264, A:D.311, PGA.7

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

NA.5: 5 residues within 4Å: Chain A: G.64, V.65, L.79, N.208, N.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.65

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

GDP.6: 19 residues within 4Å: Chain A: P.285, A.287, C.288, G.289, K.290, T.291, N.292, V.335, P.337, G.338, R.436, W.516, F.517, F.525, G.529, F.530, N.533 Ligands: MN.2, PGA.7 18 PLIP interactions: 18 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:R.436, A:F.530, A:N.533 Water bridges: A:V.335, A:R.436, A:P.528 Salt bridges: A:K.290 pi-Stacking: A:F.530, A:F.530 pi-Cation interactions: A:F.525

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

PGA.7: 14 residues within 4Å: Chain A: R.87, K.244, H.264, S.286, A.287, K.290, D.311, F.333, R.405, A.467, F.485 Ligands: MN.2, MN.4, GDP.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.286, A:A.287 Water bridges: A:K.243 Salt bridges: A:R.87, A:K.244, A:K.244, A:H.264, A:K.290, A:R.405, A:R.405

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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