SMTL ID : 6woa.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 2-Diphosphoinositol pentakisphosphate (2-IP7), Mg, and Fluoride ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

UEV.1: 19 residues within 4Å: Chain A: R.31, K.39, R.41, S.60, S.61, I.68, G.71, G.72, G.73, E.87, E.91, R.110, H.112, R.136, K.154 Ligands: MG.2, MG.3, MG.4, F.7 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:S.60, A:S.60, A:S.61, A:S.61, A:S.61, A:G.73, A:R.110 Water bridges: A:K.39, A:R.62, A:R.62, A:R.66, A:G.71, A:G.71, A:R.86, A:E.91, A:E.91, A:R.136, A:K.154, A:Q.157 Salt bridges: A:R.31, A:K.39, A:K.39, A:K.39, A:K.39, A:R.41, A:R.110, A:H.112, A:R.136, A:K.154, A:K.154

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.71, E.91 Ligands: UEV.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.71, A:E.91, A:E.91, H2O.4 MG.3: 6 residues within 4Å: Chain A: E.87, E.91 Ligands: UEV.1, MG.2, MG.4, F.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.87, A:E.91, H2O.2, H2O.3 MG.4: 4 residues within 4Å: Chain A: E.87 Ligands: UEV.1, MG.3, F.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.87, H2O.2, H2O.3, H2O.5

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

CL.5: 6 residues within 4Å: Chain A: R.48, S.49, S.51, E.52, E.53, E.54 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 7 residues within 4Å: Chain A: R.41, N.107, H.112, T.114, V.156, Q.157, Y.160 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.107, A:T.114, A:Q.157, A:Y.160 Water bridges: A:R.41, A:N.107, A:K.154, A:Q.157 Salt bridges: A:R.41, A:H.112, A:K.154

1 x F: FLUORIDE ION(Non-covalent)

F.7: 6 residues within 4Å: Chain A: E.87, E.90, E.91 Ligands: UEV.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., New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. Faseb J. (2021)

Release Date

2021-03-03

Peptides

Diphosphoinositol polyphosphate phosphohydrolase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diphosphoinositol polyphosphate phosphohydrolase 1

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