SMTL ID : 8g9e.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

ANP.1: 23 residues within 4Å: Chain A: R.98, P.113, V.149, K.151, H.158, V.160, L.175, R.177, E.201, E.202, F.203, M.204, D.210, K.212, S.228, P.229, D.273, L.275, C.284, D.285, N.287 Ligands: MG.3, MG.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:K.151, A:H.158, A:R.177, A:R.177, A:E.201, A:E.201, A:M.204, A:D.210, A:D.285, A:N.287, A:N.287 Water bridges: A:T.206, A:K.212, A:K.212, A:K.212, A:K.212, A:S.228, A:N.287 Salt bridges: A:R.98, A:K.151

1 x YUT: {difluoro[(R)-hydroxy{[(1s,2R,3S,4S,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid

YUT.2: 12 residues within 4Å: Chain A: K.17, K.18, R.177, K.178, K.212, Y.214, R.226, R.237, K.242, S.290, K.293 Ligands: MG.6 37 PLIP interactions: 37 interactions with chain A Hydrogen bonds: A:K.178, A:R.237, A:R.237, A:G.241, A:K.242, A:S.290, A:S.290 Water bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:K.18, A:S.21, A:E.156, A:R.177, A:R.177, A:R.177, A:E.243, A:R.245, A:R.245, A:R.245 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:R.177, A:K.178, A:K.212, A:R.226, A:R.226, A:K.242, A:R.245, A:K.293, A:K.293, A:K.293

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

MG.3: 4 residues within 4Å: Chain A: D.285, N.287 Ligands: ANP.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.2 MG.4: 4 residues within 4Å: Chain A: D.273, D.285 Ligands: ANP.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.3 MG.5: 3 residues within 4Å: Chain A: S.32, F.34, I.37 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.34, A:I.37, H2O.1, H2O.11, H2O.12 MG.6: 1 residues within 4Å: Ligands: YUT.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

Hostachy, S. et al., Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry (2023)

Release Date

2024-01-03

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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