SMTL ID : 1ylh.1

Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: K.233, H.252, D.289 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.252, A:D.289, H2O.6, H2O.8, H2O.8

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: L.269, S.270, G.271, T.272, G.273, K.274, T.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.269, A:G.271, A:T.272, A:G.273, A:K.274, A:T.275 PO4.3: 3 residues within 4Å: Chain A: R.174, Y.359, R.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.174 Water bridges: A:R.174, A:R.174 Salt bridges: A:R.174, A:R.366

1 x DT3: (2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1-SULFONATE(Non-covalent)

DT3.4: 5 residues within 4Å: Chain A: L.128, K.131, Q.132, C.195, T.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.131 Salt bridges: A:K.131

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 4 residues within 4Å: Chain A: C.95, K.100, W.105, P.116 No protein-ligand interaction detected (PLIP) BME.6: 4 residues within 4Å: Chain A: L.285, D.288, C.305, Y.356 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.288

1 x PYR: PYRUVIC ACID(Non-covalent)

PYR.7: 6 residues within 4Å: Chain A: R.86, Y.227, K.233, Y.306, R.353, F.433 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.86 Water bridges: A:K.232, A:K.233 Salt bridges: A:R.86, A:R.353

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.8: 5 residues within 4Å: Chain A: T.69, A.77, D.79, V.335, K.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.69, A:A.77, A:K.348 FMT.9: 6 residues within 4Å: Chain A: F.65, D.79, T.80, G.81, T.84, N.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.80, A:G.81 FMT.10: 5 residues within 4Å: Chain A: F.65, G.81, I.82, G.224, W.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.82, A:G.224 Water bridges: A:F.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leduc, Y.A. et al., Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-06-28

Peptides

phosphoenolpyruvate carboxykinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

phosphoenolpyruvate carboxykinase

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