SMTL ID : 6vcr.1

Crystal structure of E.coli RppH in complex with CTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

3 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 12 residues within 4Å: Chain A: R.28, Q.31, S.33, Q.38, G.39, Y.78, L.80, L.84, Q.96, V.138, F.140, K.141 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.28, A:Q.31, A:S.33, A:Y.78, A:Q.96 Water bridges: A:R.28, A:R.28, A:R.28, A:R.28, A:R.28, A:R.28, A:Q.38, A:Q.38, A:V.138, A:K.141 Salt bridges: A:R.28, A:R.28, A:K.141 pi-Cation interactions: A:R.28 CTP.2: 8 residues within 4Å: Chain A: N.74, W.75, L.76, R.77, D.143, V.144, R.147 Ligands: CTP.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.76 Hydrogen bonds: A:W.75, A:R.77, A:R.77, A:R.77, A:R.147 Salt bridges: A:R.147, A:R.147 CTP.3: 7 residues within 4Å: Chain A: Y.8, R.77, Y.78, K.79, D.143, R.147 Ligands: CTP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.8, A:D.143, A:R.147 Salt bridges: A:K.79, A:K.79

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.4: 3 residues within 4Å: Chain A: R.126, Y.132, Q.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.132, A:Y.132, A:Q.136, A:Q.136

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

SO4.5: 5 residues within 4Å: Chain A: T.72, R.73, N.74, L.76, E.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.73, A:N.74, A:N.74, A:E.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, A. et al., Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Nucleic Acids Res. (2020)

Release Date

2020-02-05

Peptides

RNA pyrophosphohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA pyrophosphohydrolase

Related Entries With Identical Sequence