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

Crystal structure of E. coli ApaH in complex with Up4U

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

1 x 01: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(3~{S},4~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate

01.1: 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, W.249 Ligands: MN.2, MG.3, MN.4, SO4.6 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.229 Hydrogen bonds: A:D.37, A:N.65, A:N.65, A:A.229 Water bridges: A:R.182, A:R.184, A:R.184 Salt bridges: A:H.10, A:R.41, A:R.41, A:R.41, A:H.66, A:H.66, 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

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

MN.2: 7 residues within 4Å: Chain A: D.8, H.10, D.37, D.244 Ligands: 01.1, MG.3, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.37, H2O.1, H2O.1 MN.4: 8 residues within 4Å: Chain A: D.8, D.37, N.65, H.120, H.227 Ligands: 01.1, MN.2, 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.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: D.8, H.10, D.37, D.244 Ligands: 01.1, MN.2, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.37, H2O.1, H2O.1

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

SO4.5: 1 residues within 4Å: Chain A: K.261 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.114, A:K.261, A:K.261, A:K.261, A:K.261 Salt bridges: A:K.261 SO4.6: 4 residues within 4Å: Chain A: R.41, K.83, W.249 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.41, A:R.41 Salt bridges: A:R.41 SO4.7: 2 residues within 4Å: Chain A: W.101, Q.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:Q.105

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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