SMTL ID : 3otu.1

PDK1 mutant bound to allosteric disulfide fragment activator JS30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x J30: 4-[4-(naphthalen-1-ylmethyl)piperazin-1-yl]-4-oxobutane-1-thiol(Non-covalent)

J30.1: 9 residues within 4Å: Chain A: K.72, I.76, T.85, R.88, C.105, F.106, Q.107, L.112 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.72, A:I.76, A:L.112

1 x BI4: 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE(Non-covalent)

BI4.2: 17 residues within 4Å: Chain A: L.45, G.46, V.53, A.66, K.68, Y.83, E.87, V.100, L.116, S.117, Y.118, A.119, E.123, E.166, L.169, T.179, D.180 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.45, A:V.53, A:L.116, A:E.166, A:L.169, A:T.179, A:D.180 Hydrogen bonds: A:S.117, A:A.119, A:T.179 Salt bridges: A:E.123, A:E.166

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: K.101, Y.103, S.117, Q.177 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.103, A:Y.103, A:Q.177 Water bridges: A:Y.118, A:Y.118, A:N.171 SO4.4: 4 residues within 4Å: Chain A: A.241, G.242, L.246, K.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.242 Water bridges: A:K.250, A:K.250 Salt bridges: A:K.250 SO4.5: 3 residues within 4Å: Chain A: R.240, A.241, I.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.241 SO4.6: 1 residues within 4Å: Chain A: Y.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.113 SO4.7: 2 residues within 4Å: Chain A: F.106, Q.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.107, A:Q.107 SO4.8: 3 residues within 4Å: Chain A: L.254, Y.256, F.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.254 Water bridges: A:F.258 SO4.9: 3 residues within 4Å: Chain A: D.95, Y.152, K.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.95, A:D.95 Salt bridges: A:K.156 SO4.10: 2 residues within 4Å: Chain A: Q.107 Ligands: J30.1 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: G.122, E.123, K.126 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: K.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sadowsky, J.D. et al., Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-03-23

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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