› 6ddg

Electron Microscopy
3.1Å resolution

Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-6

Released:
DOI: 10.2210/pdb6ddg/pdb
PDB entry 6ddg coloured by chain, front view.
PDB entry 6ddg coloured by chain, side view.
PDB entry 6ddg coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.
Belousoff MJ, Venugopal H, Wright A, Seoner S, Stuart I, Stubenrauch C, Bamert RS, Lupton DW, Lithgow T
ChemMedChem 14 527-531 (2019)
PMID: 30667174
Related structures: EMD-7870

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-302213 (preferred)
Entry contents:
25 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (27 distinct):
Large ribosomal subunit protein bL19 Chain: A
Molecule details ›
Chain: A
Length: 116 amino acids
Theoretical weight: 13.39 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZ42 (Residues: 1-116; Coverage: 100%)
Gene names: SAOUHSC_01211, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein uL2 Chain: B
Molecule details ›
Chain: B
Length: 276 amino acids
Theoretical weight: 30.09 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P60430 (Residues: 1-276; Coverage: 100%)
Gene names: SAOUHSC_02509, rplB
Sequence domains:
Structure domains:
Large ribosomal subunit protein bL20 Chain: C
Large ribosomal subunit protein bL21 Chain: D
Large ribosomal subunit protein uL22 Chain: E
Large ribosomal subunit protein uL23 Chain: F
Large ribosomal subunit protein uL24 Chain: G
Large ribosomal subunit protein bL25 Chain: H
Large ribosomal subunit protein bL27 Chain: I
Large ribosomal subunit protein bL28 Chain: J
Large ribosomal subunit protein uL29 Chain: K
Large ribosomal subunit protein uL3 Chain: L
Large ribosomal subunit protein uL30 Chain: M
Large ribosomal subunit protein bL32 Chain: N
Large ribosomal subunit protein bL33B Chain: O
Large ribosomal subunit protein bL34 Chain: P
Large ribosomal subunit protein bL35 Chain: Q
Large ribosomal subunit protein bL36 Chain: R
Large ribosomal subunit protein uL4 Chain: S
Large ribosomal subunit protein uL13 Chain: V
Large ribosomal subunit protein uL14 Chain: W
Large ribosomal subunit protein uL15 Chain: X
Large ribosomal subunit protein uL16 Chain: Y
Large ribosomal subunit protein bL17 Chain: Z
Large ribosomal subunit protein uL18 Chain: a
23S ribosomal RNA Chain: 1
5S ribosomal RNA Chain: 2

Ligands and Environments

1 bound ligand:
Ligand G6M 1 x G6M
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.1Å
Relevant EMDB volumes: EMD-7870

Quick links

Citations

1 review citation

The dark side of drug repurposing. From clinical trial challenges to antimicrobial resistance: analysis based on three major fields.
Natsheh et al. (2024)
5 other articles

2 mentions without citation

DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites.
Rekand et al. (2021)
1 more