SMTL ID : 6cmw.1

Crystal structure of zebrafish Phosphatidylinositol-4-phosphate 5- kinase alpha isoform with bound ATP/Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: P.108, G.109, A.110, S.111, S.113, F.115, I.124, K.126, M.176, N.177, N.178, L.179, D.191, T.212, L.258, I.332, D.333 Ligands: CA.2, CA.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.110, A:S.111, A:S.111, A:S.113, A:N.177, A:L.179, A:D.191, A:D.191, A:T.212, A:T.212, A:D.333 Salt bridges: A:K.126, A:K.126 ATP.4: 19 residues within 4Å: Chain B: P.108, G.109, A.110, S.111, S.113, F.115, I.124, K.126, M.176, N.177, N.178, L.179, D.191, T.212, L.258, I.332, D.333 Ligands: CA.5, CA.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.110, B:S.111, B:S.111, B:S.113, B:N.177, B:L.179, B:D.191, B:T.212, B:D.333 Salt bridges: B:K.126, B:K.126

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: K.193, D.254, S.256, D.333 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.333 CA.3: 3 residues within 4Å: Chain A: E.132, D.333 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.333, A:D.333 CA.5: 5 residues within 4Å: Chain B: K.193, D.254, S.256, D.333 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.333 CA.6: 3 residues within 4Å: Chain B: E.132, D.333 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.333, B:D.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, X. et al., Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5K gamma. Biochem. J. (2018)

Release Date

2018-03-14

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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