SMTL ID : 6wog.1

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 5A3: Methylenebisphosphonate inositol pentakisphosphate(Non-covalent)

5A3.1: 9 residues within 4Å: Chain A: S.60, S.61, R.62, H.63, R.66, I.68, R.110, R.136, K.154 26 PLIP interactions: 26 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:H.63, A:R.110, A:R.110, A:R.136, A:R.136, A:K.154 Water bridges: A:R.41, A:R.66, A:H.153, A:K.154 Salt bridges: A:R.62, A:H.63, A:H.63, A:H.63, A:R.66, A:R.66, A:R.110, A:R.110, A:K.154

1 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 12 PLIP interactions: 12 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:H.112 Salt bridges: A:R.41, A:R.110, A:H.112, 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

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