SMTL ID : 4s2v.1

E. coli RppH structure, KI soak

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

IOD.1: 2 residues within 4Å: Chain A: K.97 Ligands: IOD.2 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: P.10, W.75 Ligands: IOD.1 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: A.47 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: A.47, E.48 Ligand excluded by PLIP IOD.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: R.73, N.74 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: K.79, I.94 Ligand excluded by PLIP IOD.9: 5 residues within 4Å: Chain A: Y.8, R.77, Y.78, K.79 Ligands: IOD.10 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: R.77 Ligands: IOD.9 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: D.143, R.147 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: R.67 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Ligands: IOD.14 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: R.63 Ligands: IOD.13 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: R.53 Ligand excluded by PLIP IOD.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: N.18, R.19, Q.20 Ligands: IOD.18 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: N.18, R.19 Ligands: IOD.17 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: I.68 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain A: R.19 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: R.27, H.32, W.34 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: K.90, V.92 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain A: K.150 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Ligands: IOD.25, ACT.29 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain A: M.157 Ligands: IOD.24, ACT.29 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain A: W.127 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain A: W.34, Q.35, V.137, V.138 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.28: 3 residues within 4Å: Chain A: Q.38, E.54, E.58 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Q.38, A:E.54, H2O.2, H2O.2, H2O.4

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.29: 5 residues within 4Å: Chain A: W.131, K.150, A.153 Ligands: IOD.24, IOD.25 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasilyev, N. et al., Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay. J.Biol.Chem. (2015)

Release Date

2015-02-11

Peptides

RNA pyrophosphohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA pyrophosphohydrolase