SMTL ID : 4nzo.1

Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 2,5-DI-O-BN-INSP4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

ANP.1: 22 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, K.212, S.228, P.229, D.273, L.275, C.284, D.285, N.287 Ligands: MG.3, MG.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:K.151, A:H.158, A:E.201, A:E.201, A:M.204, A:D.210, A:K.212, A:D.285, A:D.285, A:N.287 Water bridges: A:Y.102, A:H.158, A:D.210, A:S.228, A:S.228, A:D.273, A:N.287 Salt bridges: A:R.98, A:K.151

1 x 2OV: (1R,2R,3r,4S,5S,6s)-3,6-bis(benzyloxy)cyclohexane-1,2,4,5-tetrayl tetrakis[dihydrogen (phosphate)](Non-covalent)

2OV.2: 7 residues within 4Å: Chain A: K.17, K.18, H.65, S.66, K.67, E.156, R.177 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.67, A:K.67, A:E.156 Hydrogen bonds: A:K.17, A:K.67 Water bridges: A:R.177 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.67, A:R.177, A:R.177

3 x MG: MAGNESIUM ION(Non-covalent)

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.9 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.7 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.6, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Synthetic Inositol Phosphate Analogs Reveal that PPIP5K2 Has a Surface-Mounted Substrate Capture Site that Is a Target for Drug Discovery. Chem.Biol. (2014)

Release Date

2014-04-02

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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