SMTL ID : 5e3t.1

Crystal structure of phosphatidylinositol-4-phosphate 5-kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 17 residues within 4Å: Chain A: G.102, S.103, F.105, I.114, K.116, N.167, N.168, L.169, D.181, K.183, T.202, D.244, L.248, I.322, D.323 Ligands: MN.2, MN.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.102, A:N.167, A:N.168, A:L.169, A:D.181, A:D.181, A:K.183, A:T.202, A:T.202 Water bridges: A:K.183 Salt bridges: A:K.116 ANP.4: 17 residues within 4Å: Chain B: G.102, S.103, F.105, I.114, K.116, N.167, N.168, L.169, D.181, K.183, T.202, D.244, L.248, I.322, D.323 Ligands: MN.5, MN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.102, B:N.167, B:N.168, B:L.169, B:D.181, B:K.183, B:T.202 Water bridges: B:K.183 Salt bridges: B:K.116

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

MN.2: 4 residues within 4Å: Chain A: D.244, D.323 Ligands: ANP.1, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.244, A:D.323, A:D.323, H2O.1 MN.3: 5 residues within 4Å: Chain A: D.244, S.246, D.323 Ligands: ANP.1, MN.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.323, H2O.1 MN.5: 4 residues within 4Å: Chain B: D.244, D.323 Ligands: ANP.4, MN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.244, B:D.323, B:D.323, H2O.1 MN.6: 5 residues within 4Å: Chain B: D.244, S.246, D.323 Ligands: ANP.4, MN.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.323, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muftuoglu, Y. et al., Mechanism of substrate specificity of phosphatidylinositol phosphate kinases. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-07-20

Peptides

Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha

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