SMTL ID : 7nnj.2 (1 other biounit)

Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: V.58, G.69, K.70, L.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.69, A:L.71

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: R.14, A.16, V.42, G.44, H.130, Y.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.14, A:R.14, A:V.42 Water bridges: A:G.44 FMT.3: 3 residues within 4Å: Chain A: R.21, V.94, W.113 No protein-ligand interaction detected (PLIP)

1 x UJN: [oxidanyl-[(2S,3R,5S,6S)-4-phenylmethoxy-2,3,5,6-tetraphosphonooxy-cyclohexyl]oxy-phosphoryl]methylphosphonic acid(Non-covalent)

UJN.4: 14 residues within 4Å: Chain A: R.4, K.12, S.33, S.34, R.35, Y.36, Q.39, I.41, G.45, G.46, R.83, R.109, H.126, K.127 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Q.39, A:H.126 Hydrogen bonds: A:R.4, A:K.12, A:K.12, A:S.34, A:S.34, A:S.34, A:R.35, A:R.35, A:G.46, A:R.109, A:K.127 Water bridges: A:E.60, A:E.64, A:K.127 Salt bridges: A:R.35, A:R.83, A:K.127, A:K.127 pi-Stacking: A:Y.36 pi-Cation interactions: A:K.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riley, A.M. et al., Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105). To Be Published

Release Date

2022-03-23

Peptides

Diphosphoinositol polyphosphate phosphohydrolase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Diphosphoinositol polyphosphate phosphohydrolase 2

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