5HL7 image
Deposition Date 2016-01-14
Release Date 2016-12-21
Last Version Date 2024-11-20
Entry Detail
PDB ID:
5HL7
Keywords:
Title:
The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lefamulin
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.55 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
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:Z (auth: 2)
Chain Length:45
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 L35
Gene (Uniprot):rpmI
Chain IDs:AA (auth: 3)
Chain Length:66
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 L36
Gene (Uniprot):rpmJ
Chain IDs:BA (auth: 4)
Chain Length:37
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 L2
Gene (Uniprot):rplB
Chain IDs:A
Chain Length:277
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 L3
Gene (Uniprot):rplC
Chain IDs:D (auth: B)
Chain Length:220
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 L4
Gene (Uniprot):rplD
Chain IDs:E (auth: C)
Chain Length:207
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 L5
Gene (Uniprot):rplE
Chain IDs:F (auth: D)
Chain Length:179
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 L6
Gene (Uniprot):rplF
Chain IDs:G (auth: E)
Chain Length:178
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 L13
Gene (Uniprot):rplM
Chain IDs:H (auth: G)
Chain Length:145
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 L14
Gene (Uniprot):rplN
Chain IDs:I (auth: H)
Chain Length:122
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 L15
Gene (Uniprot):rplO
Chain IDs:J (auth: I)
Chain Length:140
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 L16
Gene (Uniprot):rplP
Chain IDs:K (auth: J)
Chain Length:144
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 L17
Gene (Uniprot):rplQ
Chain IDs:L (auth: K)
Chain Length:122
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 L18
Gene (Uniprot):rplR
Chain IDs:M (auth: L)
Chain Length:119
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 L19
Gene (Uniprot):rplS
Chain IDs:N (auth: M)
Chain Length:116
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 L20
Gene (Uniprot):rplT
Chain IDs:O (auth: N)
Chain Length:118
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 L21
Gene (Uniprot):rplU
Chain IDs:P (auth: O)
Chain Length:102
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 L22
Gene (Uniprot):rplV
Chain IDs:Q (auth: P)
Chain Length:117
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 L23
Gene (Uniprot):rplW
Chain IDs:R (auth: Q)
Chain Length:91
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 L24
Gene (Uniprot):rplX
Chain IDs:S (auth: R)
Chain Length:105
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 L25
Gene (Uniprot):rplY
Chain IDs:T (auth: S)
Chain Length:217
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 L27
Gene (Uniprot):rpmA
Chain IDs:U (auth: T)
Chain Length:94
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 L28
Gene (Uniprot):rpmB
Chain IDs:V (auth: U)
Chain Length:62
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 L29
Gene (Uniprot):rpmC
Chain IDs:W (auth: V)
Chain Length:69
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 L30
Gene (Uniprot):rpmD
Chain IDs:X (auth: W)
Chain Length:59
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:B (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:C (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:Y (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Primary Citation
A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.
Sci Rep 6 39004 39004 (2016)
PMID: 27958389 DOI: 10.1038/srep39004

Abstact

The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug's selectivity.

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