SMTL ID : 2zkj.2 (1 other biounit)

Crystal structure of human PDK4-ADP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.241 Ligands: ADP.2, PO4.3 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: N.241 Ligands: ADP.5, PO4.6 No protein-ligand interaction detected (PLIP)

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

ADP.2: 20 residues within 4Å: Chain A: N.241, R.244, A.245, D.276, G.280, 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, PO4.3 14 PLIP interactions: 14 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.314, A:G.316, A:L.317, A:T.341 ADP.5: 21 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, Y.315, G.316, L.317, P.318, T.341 Ligands: MG.4, PO4.6 15 PLIP interactions: 15 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:G.314, B:G.314, B:G.316, B:L.317, B:T.341 Water bridges: B:A.242, B:D.276

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

PO4.3: 11 residues within 4Å: Chain A: E.237, K.240, L.310, A.311, G.312, F.313, G.314, Y.315, G.316 Ligands: MG.1, ADP.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.237, A:L.310, A:G.312, A:F.313, A:G.314, A:Y.315, A:G.316 Water bridges: A:E.237, A:E.237 Salt bridges: A:K.240 PO4.6: 11 residues within 4Å: Chain B: E.237, K.240, L.310, A.311, G.312, F.313, G.314, Y.315, G.316 Ligands: MG.4, ADP.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.312, B:F.313, B:G.314, B:Y.315, B:G.316 Water bridges: B:E.237, B:E.237, B:L.310 Salt bridges: B:K.240

Links

RCSB   PDBe   PDBe-KB   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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