SMTL ID : 8tf9.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-IP7, produced upon myo-IP6 phosphorylation by TvI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x I7P: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate(Non-covalent)

I7P.1: 20 residues within 4Å: Chain A: R.10, K.18, R.20, S.39, S.40, R.41, I.47, G.50, G.51, G.52, E.66, E.70, R.89, H.91, R.115, K.133 Ligands: MG.2, MG.3, MG.4, F.7 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.40, A:S.40, A:S.40, A:R.41, A:G.52, A:E.66, A:E.70, A:H.91, A:R.115 Water bridges: A:K.18, A:G.50, A:G.50, A:R.65, A:E.70, A:H.91, A:R.115, A:R.115, A:R.115, A:K.133, A:K.133 Salt bridges: A:R.10, A:K.18, A:K.18, A:K.18, A:R.20, A:R.41, A:R.89, A:R.115, A:K.133

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: G.50, G.51, E.66, E.70 Ligands: I7P.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.50, A:E.70, H2O.2 MG.3: 7 residues within 4Å: Chain A: E.66, E.69, E.70 Ligands: I7P.1, MG.2, MG.4, F.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.66, A:E.70, H2O.2, H2O.4 MG.4: 6 residues within 4Å: Chain A: R.65, E.66, E.69 Ligands: I7P.1, MG.3, F.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.66, H2O.2, H2O.3, H2O.5

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

CL.5: 3 residues within 4Å: Chain A: N.86, H.91, Q.136 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: R.27, S.28, E.31, E.32, E.33 Ligand excluded by PLIP

1 x F: FLUORIDE ION(Non-covalent)

F.7: 5 residues within 4Å: Chain A: E.66, E.69 Ligands: I7P.1, MG.3, MG.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zong, G. et al., Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus. Embo J. (2024)

Release Date

2023-11-15

Peptides

Diphosphoinositol polyphosphate phosphohydrolase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diphosphoinositol polyphosphate phosphohydrolase 1

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