SMTL ID : 1uu9.1

Structure of human PDK1 kinase domain in complex with BIM-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: H.68, S.120, W.276, E.277, N.278, L.279, H.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.120, A:L.279, A:H.280 Water bridges: A:S.120, A:S.120 GOL.2: 8 residues within 4Å: Chain A: S.23, K.40, L.42, Y.55, E.59, G.154 Ligands: GOL.7, SO4.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:K.40, A:E.59 Water bridges: A:G.154 GOL.3: 4 residues within 4Å: Chain A: P.8, F.13, K.83, Y.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.83 GOL.4: 4 residues within 4Å: Chain A: V.274, T.275, W.276, E.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.274, A:W.276, A:E.277 GOL.5: 4 residues within 4Å: Chain A: L.226, Y.228, F.230, R.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239 Water bridges: A:F.230 GOL.6: 3 residues within 4Å: Chain A: F.11, K.12, F.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.11, A:F.13, A:F.13 GOL.7: 8 residues within 4Å: Chain A: E.19, G.20, S.23, V.25, K.40 Ligands: GOL.2, SO4.12, BI3.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:K.40 GOL.8: 8 residues within 4Å: Chain A: R.35, E.36, Y.37, Y.75, S.89, Y.90 Ligands: SO4.10, SO4.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.35, A:Y.90 Water bridges: A:E.36, A:E.36, A:Y.37

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

SO4.9: 5 residues within 4Å: Chain A: K.5, R.60, T.77, F.78, Q.79 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.79 Water bridges: A:R.60, A:R.60, A:Q.79 Salt bridges: A:K.5, A:R.60 SO4.10: 5 residues within 4Å: Chain A: K.73, Y.75, S.89, Q.149 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.89, A:Q.149 Water bridges: A:K.73, A:K.73, A:Y.90 Salt bridges: A:K.73 SO4.11: 2 residues within 4Å: Chain A: R.35 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.35 SO4.12: 6 residues within 4Å: Chain A: G.20, S.21, F.22, S.23 Ligands: GOL.2, GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.21, A:F.22, A:S.23, A:S.23 Salt bridges: A:K.40 SO4.13: 2 residues within 4Å: Chain A: R.65, K.128 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.65, A:K.128

1 x BI3: 3-[1-(3-AMINOPROPYL)-1H-INDOL-3-YL]-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE(Non-covalent)

BI3.14: 18 residues within 4Å: Chain A: L.17, G.18, V.25, A.38, K.40, E.59, V.72, L.88, S.89, Y.90, A.91, E.95, E.138, N.139, L.141, T.151, D.152 Ligands: GOL.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.17, A:L.17, A:V.25, A:K.40, A:L.88, A:L.141, A:T.151, A:D.152 Hydrogen bonds: A:S.89, A:A.91 Water bridges: A:A.91, A:K.98, A:K.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komander, D. et al., Interactions of Ly333531 and Other Bisindolyl Maleimide Inhibitors with Pdk1. Structure (2004)

Release Date

2004-03-04

Peptides

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1