1NWY image
Deposition Date 2003-02-07
Release Date 2003-03-18
Last Version Date 2023-08-16
Entry Detail
PDB ID:
1NWY
Keywords:
Title:
COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.30 Å
R-Value Free:
0.30
R-Value Work:
0.27
R-Value Observed:
0.27
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RRNA
Chain IDs:A (auth: 0)
Chain Length:2880
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 2)
Chain Length:47
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 3)
Chain Length:65
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RRNA
Chain IDs:B (auth: 9)
Chain Length:124
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: A)
Chain Length:274
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: B)
Chain Length:211
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: C)
Chain Length:204
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: D)
Chain Length:180
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: E)
Chain Length:185
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: F)
Chain Length:146
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:I (auth: G)
Chain Length:144
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:J (auth: H)
Chain Length:174
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:K (auth: I)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:L (auth: J)
Chain Length:156
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:M (auth: K)
Chain Length:141
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:N (auth: L)
Chain Length:116
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:O (auth: M)
Chain Length:113
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:P (auth: N)
Chain Length:166
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:Q (auth: O)
Chain Length:118
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:R (auth: P)
Chain Length:100
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:S (auth: Q)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:T (auth: R)
Chain Length:94
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:U (auth: S)
Chain Length:115
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:general stress protein Ctc
Gene (Uniprot):rplY
Chain IDs:V (auth: T)
Chain Length:237
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:W (auth: U)
Chain Length:91
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: W)
Chain Length:67
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: X)
Chain Length:55
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: Y)
Chain Length:73
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Ligand Molecules
Primary Citation
Structural basis for the antibiotic activity of ketolides and azalides.
Structure 11 329 338 (2003)
PMID: 12623020 DOI: 10.1016/S0969-2126(03)00022-4

Abstact

The azalide azithromycin and the ketolide ABT-773, which were derived by chemical modifications of erythromycin, exhibit elevated activity against a number of penicillin- and macrolide-resistant pathogenic bacteria. Analysis of the crystal structures of the large ribosomal subunit from Deinococcus radiodurans complexed with azithromycin or ABT-773 indicates that, despite differences in the number and nature of their contacts with the ribosome, both compounds exert their antimicrobial activity by blocking the protein exit tunnel. In contrast to all macrolides studied so far, two molecules of azithromycin bind simultaneously to the tunnel. The additional molecule also interacts with two proteins, L4 and L22, implicated in macrolide resistance. These studies illuminated and rationalized the enhanced activity of the drugs against specific macrolide-resistant bacteria.

Legend

Protein

Chemical

Disease

Primary Citation of related structures