SMTL ID : 9on0.2 (1 other biounit)

Crystal structure of E. coli ApaH D37A mutant in complex with Ap4U

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.78, A:R.79, A:D.153 Salt bridges: A:R.79, A:D.153

1 x 01: P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate

01.2: 8 residues within 4Å: Chain A: R.41, N.65, H.66, R.184, K.197, H.227, A.229, W.249 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:K.197 Hydrogen bonds: A:N.65, A:H.227, A:A.229 Water bridges: A:R.41, A:R.41, A:R.184, A:R.184, A:R.184, A:K.197, A:H.227, A:S.230, A:S.230 Salt bridges: A:R.41, A:H.66, A:H.66, A:R.184, A:R.184, A:K.197, A:H.227

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

MN.3: 5 residues within 4Å: Chain A: D.8, H.10, A.37, H.66, H.227 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, H2O.1, H2O.3

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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