SMTL ID : 7sp3.1

E. coli RppH bound to Ap4A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x B4P: BIS(ADENOSINE)-5'-TETRAPHOSPHATE(Non-covalent)

B4P.1: 21 residues within 4Å: Chain A: R.9, N.11, R.28, S.33, Q.38, G.39, G.40, E.54, E.58, Y.78, L.80, L.84, Q.96, E.121, V.138, F.140, K.141 Ligands: MG.2, MG.3, MG.4, F.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:N.11, A:R.28, A:S.33, A:Q.38, A:Q.38, A:G.40, A:Y.78, A:Q.96 Water bridges: A:R.9, A:R.28, A:R.28, A:R.28, A:W.34, A:Q.38, A:R.53, A:K.141 Salt bridges: A:R.9, A:R.9, A:R.28, A:R.28, A:K.141 pi-Stacking: A:F.140 pi-Cation interactions: A:R.28

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.38, E.58, E.121 Ligands: B4P.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.38, A:E.58, A:E.121, H2O.3 MG.3: 8 residues within 4Å: Chain A: E.54, E.57, E.58, E.121 Ligands: B4P.1, MG.2, MG.4, F.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.54, A:E.58, A:E.121, H2O.1 MG.4: 5 residues within 4Å: Chain A: R.53, E.54 Ligands: B4P.1, MG.3, F.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.54, H2O.1, H2O.2, H2O.4

1 x F: FLUORIDE ION(Non-covalent)

F.5: 7 residues within 4Å: Chain A: E.54, E.57, E.58, E.121 Ligands: B4P.1, MG.3, MG.4 No protein-ligand interaction detected (PLIP)

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

CL.6: 1 residues within 4Å: Chain A: R.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levenson-Palmer, R. et al., A distinct RNA recognition mechanism governs Np 4 decapping by RppH. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-09

Peptides

RNA pyrophosphohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA pyrophosphohydrolase

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