SMTL ID : 7n7j.1

Crystal Structure of PI5P4KIIAlpha complex with AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 2 residues within 4Å: Chain A: D.331 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.331, H2O.1, H2O.3, H2O.5 MN.2: 3 residues within 4Å: Chain A: K.117, D.331 Ligands: ANP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.331, A:D.331, H2O.1, H2O.6 MN.7: 2 residues within 4Å: Chain B: D.331 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.331, H2O.8, H2O.10, H2O.12 MN.8: 3 residues within 4Å: Chain B: K.117, D.331 Ligands: ANP.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.331, B:D.331, H2O.8, H2O.13

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 15 residues within 4Å: Chain A: A.104, F.106, I.115, K.117, T.168, R.169, N.170, V.171, K.181, D.183, T.204, L.249, D.331 Ligands: MN.1, MN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.117, A:T.168, A:R.169, A:V.171, A:K.181, A:D.183, A:T.204, A:D.331 Water bridges: A:K.185, A:K.185 Salt bridges: A:K.117 ANP.9: 15 residues within 4Å: Chain B: A.104, F.106, I.115, K.117, T.168, R.169, N.170, V.171, K.181, D.183, T.204, L.249, D.331 Ligands: MN.7, MN.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.117, B:T.168, B:R.169, B:V.171, B:K.181, B:D.183, B:D.183, B:T.204, B:T.204, B:D.331 Water bridges: B:K.185, B:K.185, B:T.334 Salt bridges: B:K.117

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

SO4.4: 2 residues within 4Å: Chain A: K.185, R.191 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.191 Salt bridges: A:K.185, A:R.191 SO4.5: 4 residues within 4Å: Chain A: K.43, K.63, R.155 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.43, A:K.63, A:R.155 SO4.6: 5 residues within 4Å: Chain A: K.43, K.45, K.61 Chain B: K.45 Ligands: SO4.5 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.43, A:K.61, B:K.45 Water bridges: B:D.47 SO4.10: 2 residues within 4Å: Chain B: K.185, R.191 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.191 Salt bridges: B:K.185, B:R.191 SO4.11: 4 residues within 4Å: Chain B: K.43, K.63, R.155 Ligands: SO4.12 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.43, B:K.63, B:R.155 SO4.12: 5 residues within 4Å: Chain A: K.45 Chain B: K.43, K.45, K.61 Ligands: SO4.11 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.43, B:K.61, A:K.45 Water bridges: A:D.47, A:D.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Pharmacological inhibition of PI5P4K alpha / beta disrupts cell energy metabolism and selectively kills p53-null tumor cells. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-06-30

Peptides

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha

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