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PDBsum entry 3ofc
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome/antibiotic PDB id
3ofc

 

 

 

 

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Contents
Protein chains
271 a.a. *
209 a.a. *
201 a.a. *
177 a.a. *
176 a.a. *
149 a.a. *
141 a.a. *
142 a.a. *
122 a.a. *
143 a.a. *
136 a.a. *
120 a.a. *
116 a.a. *
114 a.a. *
117 a.a. *
103 a.a. *
110 a.a. *
93 a.a. *
102 a.a. *
94 a.a. *
79 a.a. *
77 a.a. *
63 a.a. *
58 a.a. *
56 a.a. *
50 a.a. *
46 a.a. *
64 a.a. *
38 a.a. *
DNA/RNA
Ligands
CLM
Metals
_MG ×140
_ZN
Waters ×654
* Residue conservation analysis
Obsolete entry
PDB id:
3ofc
Name: Ribosome/antibiotic
Title: Crystal structure of the e. Coli ribosome bound to chloramphenicol. This file contains the 50s subunit of the first 70s ribosome with chloramphenicol bound.
Structure: 23s rrna. Chain: a. 5s rrna. Chain: b. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3. Chain: d. 50s ribosomal protein l4.
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 83333. Strain: k-12. Strain: k-12
Resolution:
3.19Å     R-factor:   0.192     R-free:   0.252
Authors: J.A.Dunkle,L.Xiong,A.S.Mankin,J.H.D.Cate
Key ref: J.A.Dunkle et al. (2010). Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A, 107, 17152-17157. PubMed id: 20876128
Date:
14-Aug-10     Release date:   20-Oct-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2 from Escherichia coli (strain K12)
Seq:
Struc: 		273 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3 from Escherichia coli (strain K12)
Seq:
Struc: 		209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4 from Escherichia coli (strain K12)
Seq:
Struc: 		201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5 from Escherichia coli (strain K12)
Seq:
Struc: 		179 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6 from Escherichia coli (strain K12)
Seq:
Struc: 		177 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9 from Escherichia coli (strain K12)
Seq:
Struc: 		149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14 from Escherichia coli (strain K12)
Seq:
Struc: 		123 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15 from Escherichia coli (strain K12)
Seq:
Struc: 		144 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16 from Escherichia coli (strain K12)
Seq:
Struc: 		136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17 from Escherichia coli (strain K12)
Seq:
Struc: 		127 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18 from Escherichia coli (strain K12)
Seq:
Struc: 		117 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19 from Escherichia coli (strain K12)
Seq:
Struc: 		115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20 from Escherichia coli (strain K12)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21 from Escherichia coli (strain K12)
Seq:
Struc: 		103 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22 from Escherichia coli (strain K12)
Seq:
Struc: 		110 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23 from Escherichia coli (strain K12)
Seq:
Struc: 		100 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24 from Escherichia coli (strain K12)
Seq:
Struc: 		104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25 from Escherichia coli (strain K12)
Seq:
Struc: 		94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27 from Escherichia coli (strain K12)
Seq:
Struc: 		85 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28 from Escherichia coli (strain K12)
Seq:
Struc: 		78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29 from Escherichia coli (strain K12)
Seq:
Struc: 		63 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30 from Escherichia coli (strain K12)
Seq:
Struc: 		59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32 from Escherichia coli (strain K12)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33 from Escherichia coli (strain K12)
Seq:
Struc: 		55 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34 from Escherichia coli (strain K12)
Seq:
Struc: 		46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35 from Escherichia coli (strain K12)
Seq:
Struc: 		65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36 from Escherichia coli (strain K12)
Seq:
Struc: 		38 a.a.
38 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-G-U-U-A-A-G-C-G-A-C-U-A-A-G-C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G- ... 2854 bases
  G-C-C-U-G-G-C-G-G-C-C-G-U-A-G-C-G-C-G-G-U-G-G-U-C-C-C-A-C-C-U-G-A-C-C-C-C-A-U- 118 bases

 

 
Proc Natl Acad Sci U S A 107:17152-17157 (2010)
PubMed id: 20876128  
 
 
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
J.A.Dunkle, L.Xiong, A.S.Mankin, J.H.Cate.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
21368151 F.Yan, and D.G.Fujimori (2011).
RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift.
  Proc Natl Acad Sci U S A, 108, 3930-3934.  
21286630 G.D.Wright (2011).
Molecular mechanisms of antibiotic resistance.
  Chem Commun (Camb), 47, 4055-4061.  
21342782 L.R.Cruz-Vera, M.S.Sachs, C.L.Squires, and C.Yanofsky (2011).
Nascent polypeptide sequences that influence ribosome function.
  Curr Opin Microbiol, 14, 160-166.  
21383133 S.Chiba, T.Kanamori, T.Ueda, Y.Akiyama, K.Pogliano, and K.Ito (2011).
Recruitment of a species-specific translational arrest module to monitor different cellular processes.
  Proc Natl Acad Sci U S A, 108, 6073-6078.  
  21320180 T.Siibak, L.Peil, A.Dönhöfer, A.Tats, M.Remm, D.N.Wilson, T.Tenson, and J.Remme (2011).
Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins.
  Mol Microbiol, 80, 54-67.  
20876111 S.Douthwaite (2010).
Designer drugs for discerning bugs.
  Proc Natl Acad Sci U S A, 107, 17065-17066.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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