SMTL ID : 3hrf.1

Crystal structure of Human PDK1 kinase domain in complex with an allosteric activator bound to the PIF-pocket

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: G.41, E.42, G.43, S.44, S.46, V.48, A.61, K.63, V.95, L.111, S.112, Y.113, A.114, E.118, L.164, D.175 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.43, A:S.44, A:S.44, A:S.46, A:S.112, A:A.114, A:E.118, A:E.118 Water bridges: A:F.45, A:D.175 Salt bridges: A:K.63

1 x P47: (2Z)-5-(4-chlorophenyl)-3-phenylpent-2-enoic acid(Non-covalent)

P47.2: 11 residues within 4Å: Chain A: K.28, K.67, I.71, V.79, R.83, T.100, F.101, Q.102, L.107, Y.108, F.109 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.79, A:T.100, A:L.107, A:L.107, A:L.107, A:L.107 Hydrogen bonds: A:T.100 Water bridges: A:Q.102 Salt bridges: A:K.28, A:R.83 pi-Stacking: A:F.109

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 5 residues within 4Å: Chain A: P.259, K.260, D.263, H.291, P.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.263 Water bridges: A:K.267 Salt bridges: A:D.263 EPE.4: 5 residues within 4Å: Chain A: I.123, R.124, G.127, G.230, L.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hindie, V. et al., Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1. Nat.Chem.Biol. (2009)

Release Date

2009-09-15

Peptides

3-phosphoinositide-dependent protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-phosphoinositide-dependent protein kinase 1

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