Ligand · DI0

DI0 · Dirithromycin

DI0, Dirithromycin (C42 H78 N2 O14, 835.1 g/mol), in the MolNFT structures on GenesisL1: bound in 5 records (4 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found with it.

Component: DI0
Formula: C42 H78 N2 O14
Class: ligand
Structures: 5
PDB entries: 4

Binding sites

DI0 in 5 structures; the first of them:

6OF1 · Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin… · DI0 1A4098 · binds A746, A2058, A2059, A2062, 2MA2503, G2505, U2609, C2610 and 2 more
6XZ7 · E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and… · DI0 A3175 · binds PSU746, 5MU747, A2058, A2059, A2062, 2MA2503, G2505, U2609 and 3 more
6XZA · E. coli 70S ribosome in complex with dirithromycin, and deacylated tRNA(iMet) (focused… · DI0 A23001 · binds PSU746, 5MU747, A2058, A2059, A2062, 2MA2503, G2505, U2609 and 3 more
6XZB · E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated… · DI0 A23001 · binds PSU746, 5MU747, A2058, A2059, A2062, 2MA2503, G2505, U2609 and 3 more
6XZ7 · E. COLI 50S ribosomal subunit in complex with dirithromycin, fmet-phe- TRNA(PHE) and… · DI0 A3175 · binds PSU746, 5MU747, A2058, A2059, A2062, 2MA2503, G2505, C2610 and 1 more

Residues it binds most

A 6, C 6, U 5, 2MA 6, G 6, 5MU 4, PSU 4, LYS 3, HIS 2 (residue and the binding sites it lines).

Found with

MG · Magnesium ion
31M · 3'-deoxy-3'-[(L-methionyl-L-phenylalanyl) amino]adenosine 5'-(dihydrogen phosphate)
SF4 · Iron/sulfur cluster
K · Potassium ion
ZN · Zinc ion

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