SMTL ID : 4q4c.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and synthetic 1,5-(PP)2-IP4 (1,5-IP8)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: R.98, P.113, V.149, K.151, H.158, V.160, L.175, E.201, E.202, F.203, M.204, D.210, P.229, D.273, L.275, C.284, D.285 Ligands: I8P.2, MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.151, A:E.201, A:E.201, A:M.204, A:D.210, A:D.285 Water bridges: A:R.98, A:K.212, A:R.226 Salt bridges: A:R.98, A:R.98, A:K.151, A:H.158

1 x I8P: (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)](Non-covalent)

I8P.2: 18 residues within 4Å: Chain A: K.17, K.18, H.158, R.177, K.178, K.212, R.226, R.237, R.245, D.273, D.285, N.287, S.290, K.293 Ligands: ADP.1, MG.3, MG.4, MG.6 60 PLIP interactions: 60 interactions with chain A Hydrogen bonds: A:K.178, A:D.285, A:N.287, A:N.287, A:S.290 Water bridges: A:K.17, A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:K.18, A:K.18, A:E.156, A:R.177, A:R.177, A:K.178, A:K.178, A:K.212, A:K.212, A:K.212, A:R.226, A:R.226, A:R.226, A:R.226, A:R.226, A:R.226, A:R.237, A:E.243, A:R.245, A:R.245, A:S.290, A:S.290, A:S.290, A:F.291, A:K.293, A:K.293, A:K.293, A:K.293 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:H.158, A:R.177, A:R.177, A:R.177, A:K.178, A:K.178, A:K.178, A:K.212, A:K.212, A:K.212, A:R.226, A:R.237, A:R.245, A:K.293, A:K.293, A:K.293

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 5 residues within 4Å: Chain A: D.285, N.287 Ligands: ADP.1, I8P.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.13 MG.4: 6 residues within 4Å: Chain A: K.212, D.273, D.285 Ligands: ADP.1, I8P.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.1 MG.5: 3 residues within 4Å: Chain A: S.32, F.34, I.37 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.32, A:F.34, A:I.37, H2O.7, H2O.11 MG.6: 1 residues within 4Å: Ligands: I8P.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: N.287 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capolicchio, S. et al., Synthesis of Densely Phosphorylated Bis-1,5-Diphospho-myo-Inositol Tetrakisphosphate and its Enantiomer by Bidirectional P-Anhydride Formation. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-08-06

Peptides

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2

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