SMTL ID : 3d2r.1

Crystal structure of pyruvate dehydrogenase kinase isoform 4 in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.241 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain B: N.241 Ligands: ADP.4 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 19 residues within 4Å: Chain A: N.241, A.242, R.244, A.245, D.276, V.281, L.289, Y.294, S.295, T.296, A.311, G.312, F.313, G.314, G.316, L.317, P.318, T.341 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.241, A:R.244, A:D.276, A:S.295, A:S.295, A:T.296, A:T.296, A:G.312, A:F.313, A:G.314, A:G.316, A:L.317, A:T.341 Water bridges: A:N.241, A:A.242, A:D.276, A:L.310, A:Y.315 ADP.4: 19 residues within 4Å: Chain B: N.241, A.242, R.244, A.245, D.276, V.281, L.289, Y.294, S.295, T.296, A.311, G.312, F.313, G.314, G.316, L.317, P.318, T.341 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.241, B:R.244, B:D.276, B:S.295, B:S.295, B:T.296, B:T.296, B:G.312, B:F.313, B:G.314, B:G.316, B:L.317 Water bridges: B:N.241, B:N.241, B:A.242, B:D.276, B:L.310, B:Y.315, B:T.341, B:T.341

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.143, M.147, L.322, K.325, K.357 Chain B: W.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.325 Water bridges: A:D.143, A:D.143 GOL.6: 6 residues within 4Å: Chain A: W.378 Chain B: D.143, M.147, L.322, K.325, K.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.325, B:K.357 Water bridges: B:D.143, B:D.143

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Wynn, R.M. et al., Pyruvate Dehydrogenase Kinase-4 Structures Reveal a Metastable Open Conformation Fostering Robust Core-free Basal Activity. J.Biol.Chem. (2008)

Release Date

2008-08-05

Peptides

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4

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