SMTL ID : 9oqb.1 (1 other biounit)

Crystal structure of E. coli ApaH in complex with Up4AGG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

1 x 01- G: RNA Up4AGG

01-G.1: 16 residues within 4Å: Chain A: H.10, D.37, R.41, N.65, H.66, R.182, R.184, K.197, H.227, A.229, S.230, E.232, W.249 Ligands: MN.4, MG.5, MN.6 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:D.37, A:D.37, A:N.65, A:H.227, A:A.229, A:E.232 Water bridges: A:R.184, A:R.184, A:S.230 Salt bridges: A:H.10, A:R.41, A:R.41, A:R.41, A:H.66, A:H.66, A:R.182, A:R.184, A:R.184, A:R.184, A:R.184, A:K.197, A:K.197, A:H.227, A:H.227 pi-Stacking: A:W.249, A:W.249

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.144, S.145, D.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.146, A:D.146

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: A.218, E.219, Y.221, S.222, G.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.221 Water bridges: A:S.222, A:S.222

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

MN.4: 7 residues within 4Å: Chain A: D.8, H.10, D.37, D.244 Ligands: 01-G.1, MG.5, MN.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.37, H2O.6, H2O.6 MN.6: 7 residues within 4Å: Chain A: D.37, N.65, H.120, H.227 Ligands: 01-G.1, MN.4, MG.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:H.120, A:H.227, H2O.6

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 7 residues within 4Å: Chain A: D.8, H.10, D.37, D.244 Ligands: 01-G.1, MN.4, MN.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.37, H2O.6, H2O.6

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
A

Bis(5'-nucleosyl)-tetraphosphatase, symmetrical

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