SMTL ID : 5ygu.1

Crystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 8 residues within 4Å: Chain A: Q.72, N.157, N.190, E.208, R.209, C.217, S.219 Ligands: IOD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.72, A:N.157, A:N.190, A:E.208, A:E.208, A:S.219 Water bridges: A:N.11 Salt bridges: A:R.209

12 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: Q.72, R.209 Ligands: TLA.1 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: H.201, R.203, E.241 Ligand excluded by PLIP IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: L.149 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: G.76, R.78, C.79 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: N.11, R.78, G.218 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: R.82, R.85 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: A.71, Q.72, T.99, N.101 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: A.171 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: P.50 Chain B: R.134 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain B: R.8, L.79, Q.95 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli. Nucleic Acids Res. (2018)

Release Date

2018-06-06

Peptides

Diaminopimelate epimerase: A
RNA pyrophosphohydrolase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diaminopimelate epimerase

RNA pyrophosphohydrolase