SMTL ID : 7tn4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: G.50, G.51, E.70 Ligands: MG.2, ZM2.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.50, A:E.70, H2O.1 MG.2: 7 residues within 4Å: Chain A: E.66, E.69, E.70 Ligands: MG.1, MG.3, F.6, ZM2.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.66, A:E.70, H2O.3, H2O.3 MG.3: 4 residues within 4Å: Chain A: E.66 Ligands: MG.2, F.6, ZM2.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.66, H2O.2, H2O.3, H2O.4

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

CL.4: 3 residues within 4Å: Chain A: N.86, H.91, Q.136 Ligand excluded by PLIP CL.5: 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.6: 5 residues within 4Å: Chain A: E.66, E.69 Ligands: MG.2, MG.3, ZM2.7 No protein-ligand interaction detected (PLIP)

1 x ZM2: (1R,2S,3R,4R,5S,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate(Non-covalent)

ZM2.7: 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.1, MG.2, MG.3, F.6 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:S.40, A:S.40, A:S.40, A:R.41, A:R.41, A:R.41, A:G.52, A:R.89, A:R.115 Water bridges: A:K.18, A:K.18, A:R.20, A:R.41, A:R.41, A:G.50, A:G.50, A:R.65, A:E.70, A:H.91, A:R.115 Salt bridges: A:R.10, A:K.18, A:K.18, A:K.18, A:R.20, A:R.41, A:R.115, A:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zong, G. et al., Structural and catalytic analyses of the InsP 6 kinase activities of higher plant ITPKs. Faseb J. (2022)

Release Date

2022-06-15

Peptides

Diphosphoinositol polyphosphate phosphohydrolase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diphosphoinositol polyphosphate phosphohydrolase 1

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