RCSB PDB - 5EL6: Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin

 5EL6

Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PARClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

Rozov, A.Demeshkina, N.Khusainov, I.Westhof, E.Yusupov, M.Yusupova, G.

(2016) Nat Commun 7: 10457-10457

  • DOI: https://doi.org/10.1038/ncomms10457
  • Primary Citation of Related Structures:  
    5E7K, 5E81, 5EL4, 5EL5, 5EL6, 5EL7

  • PubMed Abstract: 

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.


  • Organizational Affiliation

    Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS/University of Strasbourg, UMR7104, 1 rue Laurent Fries, BP 10142, Illkirch 67404, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth 1E],
EB [auth 12]
256Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80371 
Go to UniProtKB:  P80371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80371
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth 2E],
FB [auth 22]
239Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80372 
Go to UniProtKB:  P80372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80372
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth 3E],
GB [auth 32]
209Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80373 
Go to UniProtKB:  P80373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80373
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth 4E],
HB [auth 42]
162Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ5 
Go to UniProtKB:  Q5SHQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth 5E],
IB [auth 52]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP8 
Go to UniProtKB:  Q5SLP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLP8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth 6E],
JB [auth 62]
156Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P17291 
Go to UniProtKB:  P17291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17291
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth 7E],
KB [auth 72]
138Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY9 
Go to UniProtKB:  P0DOY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth 8E],
LB [auth 82]
128Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80374 
Go to UniProtKB:  P80374
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80374
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth 1I],
MB [auth 1A]
105Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN7 
Go to UniProtKB:  Q5SHN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth 2I],
NB [auth 2A]
129Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80376 
Go to UniProtKB:  P80376
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80376
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth 3I],
OB [auth 3A]
132Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN3 
Go to UniProtKB:  Q5SHN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth 4I],
PB [auth 4A]
126Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80377 
Go to UniProtKB:  P80377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80377
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth 5I],
QB [auth 5A]
61Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY6 
Go to UniProtKB:  P0DOY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth 6I],
RB [auth 6A]
89Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ76 
Go to UniProtKB:  Q5SJ76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ76
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth 7I],
SB [auth 7A]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJH3 
Go to UniProtKB:  Q5SJH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJH3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth 8I],
TB [auth 8A]
105Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY7 
Go to UniProtKB:  P0DOY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth 9I],
UB [auth 9A]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLQ0 
Go to UniProtKB:  Q5SLQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AI],
VB [auth AA]
93Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP2 
Go to UniProtKB:  Q5SHP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth BI],
WB [auth BA]
106Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80380 
Go to UniProtKB:  P80380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80380
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth 1F],
XB [auth 1B]
27Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIH3 
Go to UniProtKB:  Q5SIH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIH3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1BA [auth 71],
EC [auth 79]
229Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP7 
Go to UniProtKB:  Q5SLP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLP7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth 11],
FC [auth 19]
276Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60405 
Go to UniProtKB:  P60405
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60405
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3DA [auth 21],
GC [auth 29]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN8 
Go to UniProtKB:  Q5SHN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EA [auth 31],
HC [auth 39]
210Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN9 
Go to UniProtKB:  Q5SHN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth 41],
IC [auth 49]
182Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ0 
Go to UniProtKB:  Q5SHQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth 51],
JC [auth 59]
180Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P0DOY8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY8 
Go to UniProtKB:  P0DOY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth 61],
KC [auth 69]
148Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLQ1 
Go to UniProtKB:  Q5SLQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLQ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth 58],
LC [auth 15]
140Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60488 
Go to UniProtKB:  P60488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60488
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth 68],
MC [auth 25]
122Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP8 
Go to UniProtKB:  Q5SHP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth 78],
NC [auth 35]
150Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ7 
Go to UniProtKB:  Q5SHQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth 88],
OC [auth 45]
141Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60489 
Go to UniProtKB:  P60489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60489
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth 98],
PC [auth 55]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q9Z9H5 
Go to UniProtKB:  Q9Z9H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z9H5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NA [auth A8],
QC [auth 65]
112Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ4 
Go to UniProtKB:  Q5SHQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth B8],
RC [auth 75]
146Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60490 
Go to UniProtKB:  P60490
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60490
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth C8],
SC [auth 85]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60491 
Go to UniProtKB:  P60491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60491
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth D8],
TC [auth 95]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60492 
Go to UniProtKB:  P60492
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60492
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth E8],
UC [auth A5]
113Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP3 
Go to UniProtKB:  Q5SHP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth F8],
VC [auth B5]
96Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP0 
Go to UniProtKB:  Q5SHP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth G8],
WC [auth C5]
110Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP9 
Go to UniProtKB:  Q5SHP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth H8],
XC [auth D5]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHZ1 
Go to UniProtKB:  Q5SHZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHZ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth I8],
YC [auth E5]
85Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60493 
Go to UniProtKB:  P60493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60493
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28WA [auth J8],
ZC [auth F5]
98Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P60494 
Go to UniProtKB:  P60494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60494
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AD [auth G5],
XA [auth K8]
72Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP6 
Go to UniProtKB:  Q5SHP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BD [auth H5],
YA [auth L8]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ6 
Go to UniProtKB:  Q5SHQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ZA [auth M8]71Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJE1 
Go to UniProtKB:  Q5SJE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJE1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AB [auth N8],
CD [auth J5]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80339 
Go to UniProtKB:  P80339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80339
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth P8],
DD [auth L5]
49Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80340 
Go to UniProtKB:  P80340
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80340
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth Q8],
ED [auth M5]
65Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKU1 
Go to UniProtKB:  Q5SKU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKU1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
EI [auth 13],
GDA [auth 1G]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
IDA [auth 32],
II [auth 3E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JDA [auth 5A],
MI [auth 5I],
SSA [auth C5],
XZ [auth G8]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth I8]
ABA [auth 1G]
ACA [auth 1G]
ADA [auth 1G]
AE [auth 13]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.4α = 90
b = 446β = 90
c = 617.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PARClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary