SMTL ID : 5y9a.1

Crystal structure of the complex of peptidyl tRNA hydrolase with a phosphate ion at the substrate binding site and cytarabine at a new ligand binding site at 1.1 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x AR3: CYTARABINE(Non-covalent)

AR3.1: 6 residues within 4Å: Chain A: A.21, Q.22, W.30, K.155, Q.161, D.165 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.22 Hydrogen bonds: A:K.155, A:K.155, A:D.165 Water bridges: A:Q.161

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: H.25, M.72, N.73, N.119 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.73, A:N.119 Water bridges: A:N.73, A:N.73, A:N.119 Salt bridges: A:H.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaushik, S. et al., Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies. Biochem. J. (2018)

Release Date

2017-09-13

Peptides

Peptidyl-tRNA hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidyl-tRNA hydrolase

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