SMTL ID : 2biy.1

Structure of PDK1-S241A mutant kinase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.56, E.57, Y.58, Y.96, S.110, Y.111 Ligands: SO4.12, SO4.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.56, A:Y.111 Water bridges: A:Y.58, A:K.113 GOL.2: 4 residues within 4Å: Chain A: E.144, Y.283, G.284, K.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.284, A:K.287, A:K.287 Water bridges: A:E.144, A:Y.283 GOL.3: 8 residues within 4Å: Chain A: F.43, S.44, K.61, L.63, Y.76, E.80, G.175 Ligands: ATP.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.44, A:K.61, A:K.61 Water bridges: A:F.43, A:G.175 GOL.4: 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.5: 2 residues within 4Å: Chain A: E.281, G.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.281 Water bridges: A:Y.283 GOL.6: 2 residues within 4Å: Chain A: P.257, K.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.258 GOL.7: 7 residues within 4Å: Chain A: H.89, S.141, W.297, E.298, N.299, L.300, H.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.300, A:H.301

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

SO4.8: 4 residues within 4Å: Chain A: V.295, T.296, W.297, E.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.297, A:E.298 SO4.9: 3 residues within 4Å: Chain A: K.94, Y.96 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.96 Salt bridges: A:K.94 SO4.10: 2 residues within 4Å: Chain A: R.86, K.149 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.86, A:K.149 SO4.11: 5 residues within 4Å: Chain A: K.26, R.81, T.98, F.99, Q.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.100 Water bridges: A:Q.100 Salt bridges: A:K.26, A:R.81 SO4.12: 3 residues within 4Å: Chain A: R.56 Ligands: GOL.1, SO4.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.56 SO4.13: 4 residues within 4Å: Chain A: Y.96, S.110, Q.170 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.96, A:S.110 Water bridges: A:Y.111, A:Q.170 SO4.14: 1 residues within 4Å: Chain A: R.260 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.260, A:R.260 Salt bridges: A:R.260

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

ATP.15: 17 residues within 4Å: Chain A: L.38, G.39, E.40, G.41, S.42, S.44, V.46, A.59, K.61, V.93, L.109, S.110, Y.111, A.112, E.116, L.162 Ligands: GOL.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.41, A:S.42, A:S.42, A:S.42, A:S.44, A:S.44, A:S.110, A:A.112, A:E.116, A:E.116 Water bridges: A:K.61, A:K.61 Salt bridges: A:K.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komander, D. et al., Role of T-loop phosphorylation in PDK1 activation, stability, and substrate binding. J. Biol. Chem. (2005)

Release Date

2005-02-23

Peptides

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1