SMTL ID : 6wo8.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol 1,3,4,6-tetrakisphosphate (5-PP-IP4), Mg, and Fluoride ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: 20 residues within 4Å: Chain A: R.31, K.39, R.41, S.60, S.61, R.62, 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.61, A:S.61, A:R.62, A:G.73, A:R.136 Water bridges: A:R.31, A:R.31, A:K.39, A:K.39, A:R.41, A:R.41, A:S.61, A:G.71, A:G.71, A:R.86, A:R.86, A:H.112, A:R.136, A:R.136, A:R.136, A:K.154 Salt bridges: A:R.31, A:K.39, A:K.39, A:K.39, A:R.41, A:R.110, A:H.112, A:R.136, A:K.154

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.71, G.72, E.91 Ligands: U6J.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.71, A:E.91, H2O.1 MG.3: 7 residues within 4Å: Chain A: G.71, E.87, E.91 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.87, A:E.91, H2O.3, H2O.3 MG.4: 4 residues within 4Å: Chain A: E.87 Ligands: U6J.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: 6 residues within 4Å: Chain A: R.41, N.107, H.112, V.156, Q.157, Y.160 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.41, A:N.107, A:T.114, A:Q.157, A:Q.157, A:Y.160 Water bridges: A:R.41, A:N.107, A:V.156 Salt bridges: A:H.112

1 x F: FLUORIDE ION(Non-covalent)

F.7: 5 residues within 4Å: Chain A: E.87, E.90 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., 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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