SMTL ID : 1h1w.1

High resolution crystal structure of the human PDK1 catalytic domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: F.14, I.42, K.84, Y.86 Ligand excluded by PLIP GOL.2: 10 residues within 4Å: Chain A: A.33, T.34, S.35 Chain B: H.69, S.121, W.277, E.278, N.279, L.280, H.281 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: F.12, K.13, F.14 Ligand excluded by PLIP GOL.4: 9 residues within 4Å: Chain A: R.36, E.37, Y.38, Y.76, S.90, Y.91 Ligands: SO4.10, SO4.11, GOL.20 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: K.245, L.255, M.260 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: H.281, Q.282 Chain B: S.35, R.36, E.37 Ligands: GOL.18, SO4.25 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: F.23, S.24, K.41, L.43, E.60, G.155 Ligands: ATP.14 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: L.227, Y.229, F.231, R.240 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: F.14, I.42, K.84, Y.86 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain A: H.69, S.121, W.277, E.278, N.279, L.280, H.281 Chain B: A.33, T.34, S.35 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain B: F.12, K.13, F.14 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain B: R.36, E.37, Y.38, Y.76, S.90, Y.91 Ligands: GOL.6, SO4.24, SO4.25 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: K.245, L.255, M.260 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: S.35, R.36, E.37 Chain B: H.281, Q.282 Ligands: GOL.4, SO4.11 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: F.23, S.24, K.41, L.43, E.60, G.155 Ligands: ATP.28 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: L.227, Y.229, F.231, R.240 Ligand excluded by PLIP

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

SO4.9: 5 residues within 4Å: Chain A: K.6, R.61, T.78, F.79, Q.80 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.78, A:Q.80 Water bridges: A:R.61, A:R.61, A:Q.80 Salt bridges: A:K.6, A:R.61 SO4.10: 5 residues within 4Å: Chain A: Y.76, S.90, Q.150 Ligands: GOL.4, SO4.25 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.76, A:Y.76, A:S.90, A:Q.150 Water bridges: A:Y.91, A:K.93 SO4.11: 6 residues within 4Å: Chain A: R.36 Chain B: P.70, H.281 Ligands: GOL.4, GOL.20, SO4.24 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:H.281, A:R.36 Water bridges: A:R.36, A:R.36, A:R.36 SO4.12: 4 residues within 4Å: Chain A: V.275, T.276, W.277, E.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.277, A:E.278 SO4.13: 4 residues within 4Å: Chain A: P.4, R.5 Chain B: R.66, K.129 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.5 Salt bridges: B:R.66, B:K.129 SO4.23: 5 residues within 4Å: Chain B: K.6, R.61, T.78, F.79, Q.80 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.80 Water bridges: B:R.61, B:R.61, B:Q.80 Salt bridges: B:K.6, B:R.61 SO4.24: 5 residues within 4Å: Chain B: Y.76, S.90, Q.150 Ligands: SO4.11, GOL.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.76, B:S.90, B:Q.150 Water bridges: B:Y.91, B:K.93 SO4.25: 6 residues within 4Å: Chain A: P.70, H.281 Chain B: R.36 Ligands: GOL.6, SO4.10, GOL.18 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.36, B:R.36, B:R.36 Salt bridges: B:R.36, A:H.281 SO4.26: 4 residues within 4Å: Chain B: V.275, T.276, W.277, E.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.277, B:E.278 SO4.27: 4 residues within 4Å: Chain A: R.66, K.129 Chain B: P.4, R.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.66, A:K.129 Hydrogen bonds: B:R.5

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

ATP.14: 18 residues within 4Å: Chain A: L.18, G.19, E.20, G.21, S.22, S.24, V.26, A.39, K.41, V.73, S.90, Y.91, A.92, E.96, E.139, L.142, D.153 Ligands: GOL.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.22, A:S.22, A:S.24, A:S.24, A:S.90, A:A.92, A:E.96 Water bridges: A:F.23, A:K.41, A:K.41 Salt bridges: A:K.41 ATP.28: 18 residues within 4Å: Chain B: L.18, G.19, E.20, G.21, S.22, S.24, V.26, A.39, K.41, V.73, S.90, Y.91, A.92, E.96, E.139, L.142, D.153 Ligands: GOL.21 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.22, B:S.22, B:S.24, B:S.24, B:S.90, B:A.92, B:E.96, B:E.96, B:E.139 Water bridges: B:F.23, B:K.41, B:K.41 Salt bridges: B:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biondi, R.M. et al., High Resolution Crystal Structure of the Human Pdk1 Catalytic Domain Defines the Regulatory Phosphopeptide Docking Site. Embo J. (2003)

Release Date

2003-07-17

Peptides

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1

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