SMTL ID : 8t98.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-3-PP-(1,2,4,5)IP4, Mg, and Fluoride ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x U6J: (1r,2R,3S,4r,5R,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate(Non-covalent)

U6J.1: 19 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, R.115, K.133 Ligands: MG.2, MG.3, MG.4, F.7 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:S.40, A:S.40, A:S.40, A:R.41, A:R.41, A:G.52, A:R.115 Water bridges: A:R.10, A:R.10, A:K.18, A:K.18, A:R.20, A:R.20, A:S.39, A:H.42, A:G.50, A:R.65, A:R.89, A:R.115, A:R.115, A:R.115, A:R.115, A:K.133 Salt bridges: A:R.10, A:K.18, A:K.18, A:K.18, A:R.20, 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: U6J.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: U6J.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.3, H2O.4 MG.4: 4 residues within 4Å: Chain A: E.66 Ligands: U6J.1, MG.3, F.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.66, H2O.4, H2O.4, H2O.7

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

CL.5: 4 residues within 4Å: Chain A: N.86, H.91, V.135, Q.136 Ligand excluded by PLIP CL.6: 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.7: 5 residues within 4Å: Chain A: E.66, E.69 Ligands: U6J.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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