SMTL ID : 2djh.1

Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 3PD: 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE(Non-covalent)

3PD.1: 9 residues within 4Å: Chain A: K.24, Q.28, R.32, K.59, Q.92, W.101, V.102, D.104 Ligands: UM3.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.28, A:V.102, A:V.102, A:V.102 Water bridges: A:K.24, A:K.59, A:Q.92, A:Q.92 Salt bridges: A:K.24, A:R.32, A:K.59 pi-Stacking: A:W.101 pi-Cation interactions: A:W.101

1 x UM3: 2'-DEOXYURIDINE 3'-MONOPHOSPHATE(Non-covalent)

UM3.2: 14 residues within 4Å: Chain A: S.51, F.52, D.53, K.54, R.55, S.56, K.59, V.82, T.91, Q.92, D.104, R.106, I.107 Ligands: 3PD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.92, A:D.104 Hydrogen bonds: A:K.24, A:S.51, A:F.52, A:K.54, A:S.56 Water bridges: A:K.54, A:S.56, A:K.58, A:K.58 Salt bridges: A:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yajima, S. et al., Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction. Nucleic Acids Res. (2006)

Release Date

2007-01-23

Peptides

Colicin-E5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Colicin-E5

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