SMTL ID : 6woh.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1,5-di-methylenebisphosphonate inositol tetrakisphosphate (1,5-PCP-IP4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 4WZ: {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)(Non-covalent)

4WZ.1: 10 residues within 4Å: Chain A: S.60, S.61, R.62, H.63, R.66, I.68, R.110, R.136, H.153, K.154 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.60, A:S.60, A:S.60, A:S.61, A:S.61, A:S.61, A:R.62, A:R.62, A:H.63, A:R.110, A:R.110, A:R.136, A:R.136, A:H.153, A:K.154 Water bridges: A:R.66, A:R.66, A:R.66, A:R.66, A:K.154 Salt bridges: A:R.62, A:R.62, A:H.63, A:H.63, A:H.63, A:R.66, A:R.66, A:R.110, A:K.154

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

SO4.2: 7 residues within 4Å: Chain A: R.41, N.107, R.110, H.112, K.154, Q.157, Y.160 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.107, A:Q.157, A:Y.160 Water bridges: A:R.41, A:R.41, A:R.41, A:N.107, A:T.114, A:T.114, A:T.114 Salt bridges: A:R.41, A:R.110, A:H.112, A:K.154 SO4.3: 5 residues within 4Å: Chain A: K.39, R.41, G.72, G.73, H.112 6 PLIP interactions: 6 interactions with chain A Water bridges: A:G.73, A:G.73, A:R.110 Salt bridges: A:K.39, A:R.41, A:H.112

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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