SMTL ID : 1uu7.1

Structure of human PDK1 kinase domain in complex with BIM-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: P.29, F.34, K.104, Y.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.104, A:K.104, A:Y.106 Water bridges: A:P.29 GOL.2: 3 residues within 4Å: Chain A: F.32, K.33, F.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.32, A:F.34 GOL.3: 8 residues within 4Å: Chain A: R.56, E.57, Y.58, Y.96, S.110, Y.111 Ligands: SO4.7, SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.56, A:Y.111 Water bridges: A:E.57, A:E.57 GOL.4: 8 residues within 4Å: Chain A: H.89, S.141, W.297, E.298, N.299, L.300, H.301, Q.302 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.141, A:L.300, A:H.301, A:Q.302 Water bridges: A:S.141, A:S.141

1 x BI2: 3-(1H-INDOL-3-YL)-4-(1-{2-[(2S)-1-METHYLPYRROLIDINYL]ETHYL}-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE(Non-covalent)

BI2.5: 16 residues within 4Å: Chain A: L.38, G.39, A.59, K.61, E.80, V.93, L.109, S.110, Y.111, A.112, E.116, E.159, N.160, L.162, T.172, D.173 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.38, A:K.61, A:L.109, A:E.159, A:L.162, A:T.172, A:D.173 Hydrogen bonds: A:S.110, A:A.112, A:T.172 Water bridges: A:E.159 Salt bridges: A:E.116, A:E.159

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

SO4.6: 5 residues within 4Å: Chain A: K.26, R.81, T.98, F.99, Q.100 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.98, A:T.98, A:Q.100 Water bridges: A:R.81, A:R.81 Salt bridges: A:K.26, A:R.81 SO4.7: 4 residues within 4Å: Chain A: Y.96, S.110, Q.170 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.96, A:Y.96, A:S.110, A:S.110, A:Q.170 SO4.8: 2 residues within 4Å: Chain A: R.56 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.56 SO4.9: 4 residues within 4Å: Chain A: G.41, S.42, F.43, S.44 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.42, A:F.43, A:S.44, A:S.44 Water bridges: A:S.44, A:S.44 Salt bridges: A:K.61

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

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