SMTL ID : 9ojd.2 (1 other biounit)

Crystal structure of E. coli diadenosine tetraphosphate hydrolase (ApaH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 5 residues within 4Å: Chain A: I.77, S.78, R.79, D.153, Y.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.79, A:D.153 Salt bridges: A:R.79, A:D.153

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: D.8, D.37, N.65, H.120, H.227 Ligands: MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:H.120, A:H.227, H2O.7

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.8, H.10, D.37 Ligands: MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.37, H2O.3, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuthanakanti, A. et al., ApaH decaps Np 4 N-capped RNAs in two alternative orientations. Nat.Chem.Biol. (2025)

Release Date

2025-09-03

Peptides

Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]

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