SMTL ID : 8g9c.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- difluoromethylenebisphosphonate inositol pentakisphosphate (5-PCF2P-IP5), an analogue of 5-InsP7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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.1: 16 residues within 4Å: Chain A: R.10, K.18, R.20, S.39, S.40, R.41, H.42, I.47, G.50, G.51, E.70, R.89, R.115, K.133 Ligands: MG.2, MG.5 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:S.39, A:S.40, A:S.40, A:S.40, A:R.41, A:H.42, A:E.70, A:R.89, A:K.133 Water bridges: A:K.18, A:R.20, A:G.50, A:G.50, A:G.52, A:G.52, A:E.70, A:E.70, A:H.91, A:R.115, A:K.133 Salt bridges: A:R.10, A:K.18, A:K.18, A:R.20, A:R.89, A:R.115, A:K.133

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

MG.2: 6 residues within 4Å: Chain A: G.50, G.51, E.70 Ligands: YUT.1, MG.3, MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.50, A:E.70, H2O.1, H2O.3 MG.3: 6 residues within 4Å: Chain A: E.66, E.70 Ligands: MG.2, MG.4, MG.5, F.8 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.66, A:E.70, H2O.1, H2O.1, H2O.3 MG.4: 6 residues within 4Å: Chain A: R.65, E.66, E.69 Ligands: MG.3, MG.5, F.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.66, H2O.1, H2O.1, H2O.2, H2O.4 MG.5: 5 residues within 4Å: Ligands: YUT.1, MG.2, MG.3, MG.4, F.8 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: N.86, H.91, Q.136 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: R.27, S.28, S.30, E.31, E.32, E.33 Ligand excluded by PLIP

1 x F: FLUORIDE ION(Non-covalent)

F.8: 5 residues within 4Å: Chain A: E.66, E.69 Ligands: MG.3, MG.4, MG.5 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

Diphosphoinositol polyphosphate phosphohydrolase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diphosphoinositol polyphosphate phosphohydrolase 1

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