SMTL ID : 7aur.1

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 14 residues within 4Å: Chain A: R.35, S.55, S.56, A.57, I.63, K.66, D.103, T.133, F.135, R.155, R.174, E.176 Ligands: ANP.2, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.35, A:S.55, A:S.56, A:S.56, A:S.56, A:A.57, A:D.103, A:R.155, A:R.155 Water bridges: A:S.55, A:K.66, A:R.174, A:R.174, A:R.174 Salt bridges: A:K.66, A:R.174 ANP.2: 8 residues within 4Å: Chain A: H.58, R.61, D.103, R.105, P.106, K.173, R.174 Ligands: ANP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.61, A:R.61, A:R.105, A:K.173 Water bridges: A:H.58 ANP.3: 3 residues within 4Å: Chain A: L.98, G.99, R.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.183 Water bridges: A:T.100 pi-Cation interactions: A:R.183

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: R.35 Ligands: ANP.1, CL.6 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: E.83 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.83, H2O.1, H2O.1, H2O.2, H2O.4

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

CL.6: 5 residues within 4Å: Chain A: R.35, V.37, K.66, G.67 Ligands: MG.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marquez-Monino, M.A. et al., Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping. Sci Adv (2021)

Release Date

2021-05-19

Peptides

Diphosphoinositol polyphosphate phosphohydrolase DDP1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diphosphoinositol polyphosphate phosphohydrolase DDP1

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