3CPW image
Entry Detail
PDB ID:
3CPW
Keywords:
RIBOSOME
Title:
The structure of the antibiotic LINEZOLID bound to the large ribosomal subunit of HALOARCULA MARISMORTUI
Biological Source:
Source Organism:
HALOARCULA MARISMORTUI
PDB Version:
Deposition Date:
2008-04-01
Release Date:
2008-07-22
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.70 Å
R-Value Free:
0.23
R-Value Work:
0.19
Space Group:
C 2 2 21
3CPW validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:23S RIBOSOMAL RNA
Mutations:G2099A
Chain IDs:A (auth: 0)
Chain Length:2922
Number of Molecules:1
Biological Source:HALOARCULA MARISMORTUI
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L39e
Chain IDs:CA (auth: 1)
Chain Length:50
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22452 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L44E
Chain IDs:DA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32411 Pfam ID:PF00935
Polymer Type:polyribonucleotide
Description:5'-R(*CP*CP*AP*(PHE)*(ACA))-3'
Chain IDs:EA (auth: 4)
Chain Length:4
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polyribonucleotide
Description:5S RIBOSOMAL RNA
Chain IDs:B (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:HALOARCULA MARISMORTUI
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2P
Chain IDs:C (auth: A)
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20276 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3P
Chain IDs:D (auth: B)
Chain Length:338
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20279 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4P
Chain IDs:E (auth: C)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12735 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5P
Chain IDs:F (auth: D)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14124 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6P
Chain IDs:G (auth: E)
Chain Length:178
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14135 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L7Ae
Chain IDs:H (auth: F)
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12743 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L10E
Chain IDs:I (auth: G)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P15825 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L10e
Chain IDs:J (auth: H)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60617 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13P
Chain IDs:K (auth: I)
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P29198 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14P
Chain IDs:L (auth: J)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22450 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15P
Chain IDs:M (auth: K)
Chain Length:165
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12737 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15e
Chain IDs:N (auth: L)
Chain Length:196
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60618 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18P
Chain IDs:O (auth: M)
Chain Length:187
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14123 Pfam ID:PF17144
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18e
Chain IDs:P (auth: N)
Chain Length:116
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12733 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19e
Chain IDs:Q (auth: O)
Chain Length:149
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14119 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21e
Chain IDs:R (auth: P)
Chain Length:96
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12734 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22P
Chain IDs:S (auth: Q)
Chain Length:155
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10970 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23P
Chain IDs:T (auth: R)
Chain Length:85
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12732 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24P
Chain IDs:U (auth: S)
Chain Length:120
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10972 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24e
Chain IDs:V (auth: T)
Chain Length:67
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14116 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29P
Chain IDs:W (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10971 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30P
Chain IDs:X (auth: V)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14121 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31e
Chain IDs:Y (auth: W)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P18138 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32e
Chain IDs:Z (auth: X)
Chain Length:241
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12736 Pfam ID:PF14520, PF01655
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L37Ae
Chain IDs:AA (auth: Y)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60619 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L37e
Chain IDs:BA (auth: Z)
Chain Length:57
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32410 Pfam ID:PF01907
Ligand Molecules
ACE
CD
CL
K
MG
NA
SR
ZLD
Primary Citation
Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit
J.Med.Chem. 51 3353 3356 (2008)
PMID: 18494460 DOI: 10.1021/jm800379d

Abstact

The oxazolidinone antibacterials target the 50S subunit of prokaryotic ribosomes. To gain insight into their mechanism of action, the crystal structure of the canonical oxazolidinone, linezolid, has been determined bound to the Haloarcula marismortui 50S subunit. Linezolid binds the 50S A-site, near the catalytic center, which suggests that inhibition involves competition with incoming A-site substrates. These results provide a structural basis for the discovery of improved oxazolidinones active against emerging drug-resistant clinical strains.

Legend

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Disease

Primary Citation of related structures
3CPW