SMTL ID : 6wof.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 20min in the absence of Fluoride.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 6 residues within 4Å: Chain A: G.71, G.72, E.91 Ligands: MG.2, MG.3, IHP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.71, A:E.91, H2O.1, H2O.1 MG.2: 6 residues within 4Å: Chain A: G.71, E.87, E.91 Ligands: MG.1, MG.3, IHP.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.87, H2O.1, H2O.1, H2O.4, H2O.6 MG.3: 3 residues within 4Å: Ligands: MG.1, MG.2, IHP.6 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: N.107, H.112, Q.157 Ligand excluded by PLIP 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 IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.6: 18 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.91, R.110, H.112, R.136, K.154 Ligands: MG.1, MG.2, MG.3 26 PLIP interactions: 26 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:S.60, A:G.71, A:H.112, A:R.136, A:K.154, A:K.154, A:K.154, A:K.154 Salt bridges: A:R.31, A:K.39, A:K.39, A:R.41, A:R.62, A:R.110, A:H.112, A:R.136, A:K.154

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

Related Entries With Identical Sequence