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PDBsum entry 3i55

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome/antibiotic PDB id
3i55
Jmol
Contents
Protein chains
237 a.a. *
337 a.a. *
246 a.a. *
140 a.a. *
172 a.a. *
119 a.a. *
29 a.a. *
160 a.a. *
70 a.a. *
142 a.a. *
132 a.a. *
145 a.a. *
194 a.a. *
186 a.a. *
115 a.a. *
143 a.a. *
95 a.a. *
150 a.a. *
81 a.a. *
119 a.a. *
53 a.a. *
65 a.a. *
154 a.a. *
82 a.a. *
142 a.a. *
73 a.a. *
56 a.a. *
46 a.a. *
92 a.a. *
DNA/RNA
Ligands
MYL
Metals
_SR ×108
_NA ×75
_CL ×22
_MG ×93
_CD ×5
__K ×2
Waters ×7823
* Residue conservation analysis
PDB id:
3i55
Name: Ribosome/antibiotic
Title: Co-crystal structure of mycalamide a bound to the large ribosomal subunit
Structure: 23s ribosomal RNA. Chain: 0. 50s ribosomal protein l2p. Chain: a. Synonym: hmal2, hl4. 50s ribosomal protein l3p. Chain: b. Synonym: hmal3, hl1. 50s ribosomal protein l4p.
Source: Haloarcula marismortui atcc 43049. Organism_taxid: 272569. Haloarcula marismortui. Halobacterium marismortui. Organism_taxid: 2238. Synthetic: yes
Resolution:
3.11Å     R-factor:   0.210     R-free:   0.260
Authors: G.Gurel,G.Blaha,T.A.Steitz,P.B.Moore
Key ref: G.Gürel et al. (2009). Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui. Antimicrob Agents Chemother, 53, 5010-5014. PubMed id: 19738021
Date:
03-Jul-09     Release date:   09-Mar-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  50S ribosomal protein L2
Seq:
Struc:
240 a.a.
237 a.a.
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  50S ribosomal protein L3
Seq:
Struc:
338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  50S ribosomal protein L4
Seq:
Struc:
246 a.a.
246 a.a.
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  50S ribosomal protein L5
Seq:
Struc:
177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  50S ribosomal protein L6
Seq:
Struc:
178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  50S ribosomal protein L7Ae
Seq:
Struc:
120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P15825  (RLA0_HALMA) -  50S ribosomal protein L10
Seq:
Struc:
348 a.a.
29 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10_HALMA) -  50S ribosomal protein L10e
Seq:
Struc:
177 a.a.
160 a.a.
Protein chain
Pfam   ArchSchema ?
P14122  (RL11_HALMA) -  50S ribosomal protein L11
Seq:
Struc:
162 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  50S ribosomal protein L13
Seq:
Struc:
145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  50S ribosomal protein L14
Seq:
Struc:
132 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  50S ribosomal protein L15
Seq:
Struc:
165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  50S ribosomal protein L15e
Seq:
Struc:
196 a.a.
194 a.a.
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  50S ribosomal protein L18
Seq:
Struc:
187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  50S ribosomal protein L18e
Seq:
Struc:
116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19_HALMA) -  50S ribosomal protein L19e
Seq:
Struc:
149 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  50S ribosomal protein L21e
Seq:
Struc:
96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  50S ribosomal protein L22
Seq:
Struc:
155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  50S ribosomal protein L23P
Seq:
Struc:
85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  50S ribosomal protein L24P
Seq:
Struc:
120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  50S ribosomal protein L24e
Seq:
Struc:
67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  50S ribosomal protein L29P
Seq:
Struc:
71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  50S ribosomal protein L30P
Seq:
Struc:
154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  50S ribosomal protein L31e
Seq:
Struc:
92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  50S ribosomal protein L32e
Seq:
Struc:
241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  50S ribosomal protein L37Ae
Seq:
Struc:
92 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  50S ribosomal protein L37e
Seq:
Struc:
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  50S ribosomal protein L39e
Seq:
Struc:
50 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P32411  (RL44_HALMA) -  50S ribosomal protein L44e
Seq:
Struc:
92 a.a.
92 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     ribosome biogenesis   7 terms 
  Biochemical function     structural constituent of ribosome     11 terms  

 

 
Antimicrob Agents Chemother 53:5010-5014 (2009)
PubMed id: 19738021  
 
 
Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.
G.Gürel, G.Blaha, T.A.Steitz, P.B.Moore.
 
  ABSTRACT  
 
Structures have been obtained for the complexes that triacetyloleandomycin and mycalamide A form with the large ribosomal subunit of Haloarcula marismortui. Triacetyloleandomycin binds in the nascent peptide tunnel and inhibits the activity of ribosomes by blocking the growth of the nascent peptide chain. Mycalamide A binds to the E site and inhibits protein synthesis by occupying the space normally occupied by the CCA end of E-site-bound tRNAs.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21116410 S.Sagar, M.Kaur, and K.P.Minneman (2010).
Antiviral lead compounds from marine sponges.
  Mar Drugs, 8, 2619-2638.  
20154667 T.Schneider-Poetsch, T.Usui, D.Kaida, and M.Yoshida (2010).
Garbled messages and corrupted translations.
  Nat Chem Biol, 6, 189-198.  
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.