SMTL ID : 7l3m.1

PEPCK MMQX structure 40ms post-mixing with oxaloacetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: K.246, H.266, D.313 Ligands: PEP.3 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.266, A:D.313, H2O.1, PEP.3 MN.6: 4 residues within 4Å: Chain A: T.293, D.312 Ligands: PEP.3, GDP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.293, H2O.1, H2O.2, H2O.8 MN.7: 2 residues within 4Å: Chain A: H.504, E.609 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.504, A:E.609, A:E.609, H2O.3

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

NA.2: 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:N.210

1 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.3: 13 residues within 4Å: Chain A: R.89, K.246, H.266, S.288, A.289, K.292, D.313, R.407, F.487 Ligands: MN.1, GDP.4, CO2.5, MN.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.288, A:A.289 Water bridges: A:R.89, A:S.288, A:V.337, A:R.407, A:R.407, A:R.407 Salt bridges: A:R.89, A:K.246, A:K.246, A:H.266, A:K.292, A:K.292, A:R.407

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

GDP.4: 17 residues within 4Å: Chain A: P.287, A.289, C.290, G.291, K.292, T.293, N.294, G.340, R.438, W.518, F.519, F.527, G.531, F.532, N.535 Ligands: PEP.3, MN.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.289, A:C.290, A:G.291, A:K.292, A:T.293, A:N.294, A:N.294, A:G.340, A:R.438, A:F.532, A:N.535 Water bridges: A:T.293, A:V.337, A:P.530 Salt bridges: A:K.292 pi-Stacking: A:F.532, A:F.532 pi-Cation interactions: A:F.527

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.5: 7 residues within 4Å: Chain A: R.89, Y.237, G.239, F.335, N.405, R.407 Ligands: PEP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.89, A:G.239, A:N.405

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clinger, J.A. et al., Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection. Iucrj (2021)

Release Date

2021-10-13

Peptides

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoenolpyruvate carboxykinase, cytosolic [GTP]

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