5NRG image
Deposition Date 2017-04-23
Release Date 2017-08-09
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5NRG
Keywords:
Title:
The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with RB02
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.44 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 65 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:Y (auth: 2)
Chain Length:45
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:Z (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: A)
Chain Length:277
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: B)
Chain Length:220
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: C)
Chain Length:207
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: D)
Chain Length:179
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: E)
Chain Length:178
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:H (auth: G)
Chain Length:145
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:I (auth: H)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:J (auth: I)
Chain Length:140
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:K (auth: J)
Chain Length:144
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:L (auth: K)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:M (auth: L)
Chain Length:119
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:N (auth: M)
Chain Length:116
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:O (auth: N)
Chain Length:118
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:P (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Q (auth: P)
Chain Length:117
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:R (auth: Q)
Chain Length:91
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:S (auth: R)
Chain Length:105
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:T (auth: S)
Chain Length:217
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:U (auth: T)
Chain Length:94
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:V
Chain Length:69
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:W
Chain Length:59
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: X)
Chain Length:2923
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: Y)
Chain Length:114
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:X (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Primary Citation
Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
Nucleic Acids Res. 45 10284 10292 (2017)
PMID: 28973455 DOI: 10.1093/nar/gkx658

Abstact

Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen. This small, albeit important group of antibiotics is mostly active against Gram-positive bacteria, but also used against selected Gram-negative anaerobes and protozoa. S. aureus resistance to lincosamides can be acquired by modifications and/or mutations in the rRNA and rProteins. Here, we present the crystal structures of the large ribosomal subunit of S. aureus in complex with the lincosamides lincomycin and RB02, a novel semisynthetic derivative and discuss the biochemical aspects of the in vitro potency of various lincosamides. These results allow better understanding of the drugs selectivity as well as the importance of the various chemical moieties of the drug for binding and inhibition.

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