› 4ioa

X-ray diffraction
3.2Å resolution

Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans

Released:
DOI: 10.2210/pdb4ioa/pdb
Model geometry
Fit model/data
PDB entry 4ioa coloured by chain, front view.
PDB entry 4ioa coloured by chain, side view.
PDB entry 4ioa coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.
Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V
Bioorg Med Chem Lett 23 1727-31 (2013)
PMID: 23414806

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-302827 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 29.98 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ9 (Residues: 2-275; Coverage: 100%)
Gene names: DR_0314, rplB
Sequence domains:
Structure domains: Nucleic acid-binding proteins
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 211 amino acids
Theoretical weight: 22.48 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-211; Coverage: 100%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Large ribosomal subunit protein uL5 Chain: D
Large ribosomal subunit protein uL6 Chain: E
Large ribosomal subunit protein uL11 Chain: F
Large ribosomal subunit protein uL13 Chain: G
Large ribosomal subunit protein uL14 Chain: H
Large ribosomal subunit protein uL15 Chain: I
Large ribosomal subunit protein uL16 Chain: J
Large ribosomal subunit protein bL17 Chain: K
Large ribosomal subunit protein uL18 Chain: L
Large ribosomal subunit protein bL19 Chain: M
Large ribosomal subunit protein bL20 Chain: N
Large ribosomal subunit protein bL21 Chain: O
Large ribosomal subunit protein uL22 Chain: P
Large ribosomal subunit protein uL23 Chain: Q
Large ribosomal subunit protein uL24 Chain: R
Large ribosomal subunit protein bL25 Chain: S
Large ribosomal subunit protein bL27 Chain: T
Large ribosomal subunit protein bL28 Chain: U
Large ribosomal subunit protein uL29 Chain: V
Large ribosomal subunit protein uL30 Chain: W
Large ribosomal subunit protein bL32 Chain: Z
Large ribosomal subunit protein bL33 Chain: 1
Large ribosomal subunit protein bL34 Chain: 2
Large ribosomal subunit protein bL35 Chain: 3
Large ribosomal subunit protein bL36 Chain: 4
23S ribosomal RNA Chain: X
5S ribosomal RNA Chain: Y

Ligands and Environments

2 bound ligands:
Ligand MG 35 x MG
Ligand 1F3 1 x 1F3
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: I222
Unit cell:
a: 169.767Å b: 406.661Å c: 696.738Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.23

Quick links

Citations

2 review citations

Recent advances in the discovery and combinatorial biosynthesis of microbial 14-membered macrolides and macrolactones.
Park et al. (2019)
1 more

5 mentions without citation

The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.
Parlea et al. (2016)
4 more