6N9F

Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic ACCA-DPhe and bound to mRNA and P-site tRNA at 3.7A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.

Melnikov, S.V.Khabibullina, N.F.Mairhofer, E.Vargas-Rodriguez, O.Reynolds, N.M.Micura, R.Soll, D.Polikanov, Y.S.

(2019) Nucleic Acids Res 47: 2089-2100

  • DOI: 10.1093/nar/gky1211
  • Primary Citation of Related Structures:  
    6N9E, 6N9F

  • PubMed Abstract: 
  • During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids ...

    During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.


    Organizational Affiliation

    Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L2C [auth 1D],
FB [auth 2D]
276Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L3D [auth 1E],
GB [auth 2E]
206Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L4E [auth 1F],
HB [auth 2F]
210Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L5F [auth 1G],
IB [auth 2G]
182Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L6G [auth 1H],
JB [auth 2H]
180Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L9H [auth 1I],
KB [auth 2I]
148Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L13I [auth 1N],
LB [auth 2N]
140Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L14J [auth 1O],
MB [auth 2O]
122Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L15K [auth 1P],
NB [auth 2P]
150Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L16L [auth 1Q],
OB [auth 2Q]
141Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L17M [auth 1R],
PB [auth 2R]
118Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L18N [auth 1S],
QB [auth 2S]
112Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L19O [auth 1T],
RB [auth 2T]
146Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L20P [auth 1U],
SB [auth 2U]
118Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L21Q [auth 1V],
TB [auth 2V]
101Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L22R [auth 1W],
UB [auth 2W]
113Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L23S [auth 1X],
VB [auth 2X]
96Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth 1Y],
WB [auth 2Y]
110Thermus thermophilusMutation(s): 0 
Gene Names: rplXrpl24
UniProt
Find proteins for Q56435 (Thermus thermophilus)
Explore Q56435 
Go to UniProtKB:  Q56435
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56435
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth 1Z],
XB [auth 2Z]
206Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q72IA7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72IA7 
Go to UniProtKB:  Q72IA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72IA7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth 10],
YB [auth 20]
85Thermus thermophilusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth 11],
ZB [auth 21]
98Thermus thermophilusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth 12],
AC [auth 22]
72Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q72I12 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72I12 
Go to UniProtKB:  Q72I12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72I12
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth 13],
BC [auth 23]
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmDrpl30
UniProt
Find proteins for P74909 (Thermus thermophilus)
Explore P74909 
Go to UniProtKB:  P74909
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74909
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31Z [auth 14],
CC [auth 24]
71Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q72JR0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72JR0 
Go to UniProtKB:  Q72JR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72JR0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth 15],
DC [auth 25]
60Thermus thermophilusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth 16],
EC [auth 26]
54Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q72GW3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GW3 
Go to UniProtKB:  Q72GW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72GW3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth 17],
FC [auth 27]
49Thermus thermophilusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L35DA [auth 18],
GC [auth 28]
65Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L36EA [auth 19],
HC [auth 29]
37Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S2GA [auth 1b],
JC [auth 2b]
256Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S3HA [auth 1c],
KC [auth 2c]
239Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S4IA [auth 1d],
LC [auth 2d]
209Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S5JA [auth 1e],
MC [auth 2e]
162Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S6KA [auth 1f],
NC [auth 2f]
101Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S7LA [auth 1g],
OC [auth 2g]
156Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S8MA [auth 1h],
PC [auth 2h]
138Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth 1i],
QC [auth 2i]
128Thermus thermophilusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10OA [auth 1j],
RC [auth 2j]
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJrps10
UniProt
Find proteins for P80375 (Thermus thermophilus)
Explore P80375 
Go to UniProtKB:  P80375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80375
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11PA [auth 1k],
SC [auth 2k]
129Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P62654 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P62654 
Go to UniProtKB:  P62654
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62654
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth 1l],
TC [auth 2l]
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsLrps12
UniProt
Find proteins for P17293 (Thermus thermophilus)
Explore P17293 
Go to UniProtKB:  P17293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17293
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth 1m],
UC [auth 2m]
126Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P62655 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P62655 
Go to UniProtKB:  P62655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62655
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZSA [auth 1n],
VC [auth 2n]
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZrps14rpsN
UniProt
Find proteins for P24320 (Thermus thermophilus)
Explore P24320 
Go to UniProtKB:  P24320
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24320
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth 1o],
WC [auth 2o]
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsOrps15
UniProt
Find proteins for P80378 (Thermus thermophilus)
Explore P80378 
Go to UniProtKB:  P80378
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80378
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth 1p],
XC [auth 2p]
88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P62238 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P62238 
Go to UniProtKB:  P62238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62238
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth 1q],
YC [auth 2q]
105Thermus thermophilusMutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth 1r],
ZC [auth 2r]
88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P62659 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P62659 
Go to UniProtKB:  P62659
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62659
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S19XA [auth 1s],
AD [auth 2s]
93Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S20YA [auth 1t],
BD [auth 2t]
106Thermus thermophilusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxZA [auth 1u],
CD [auth 2u]
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsU
UniProt
Find proteins for P62612 (Thermus thermophilus)
Explore P62612 
Go to UniProtKB:  P62612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62612
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA [auth 1A],
DB [auth 2A]
2915Thermus thermophilus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAB [auth 1B],
EB [auth 2B]
121Thermus thermophilus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAFA [auth 1a],
IC [auth 2a]
1521Thermus thermophilus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChainsLengthOrganismImage
mRNAAB [auth 1v],
DD [auth 2v]
24Escherichia virus T4
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 54
MoleculeChainsLengthOrganismImage
ACCA-DPheBB [auth 1w],
ED [auth 2w]
4Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChainsLengthOrganismImage
P-site tRNA, Deacylated Initiator Methionyl-tRNACB [auth 1x],
FD [auth 2x]
77Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
FEA [auth 1d],
XCB [auth 2d]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CAA [auth 1Y],
DDB [auth 2n],
EYA [auth 24],
GYA [auth 25],
HYA [auth 26],
CAA [auth 1Y],
DDB [auth 2n],
EYA [auth 24],
GYA [auth 25],
HYA [auth 26],
IAA [auth 14],
IEA [auth 1n],
KAA [auth 15],
LYA [auth 29],
MAA [auth 16],
SAA [auth 19],
ZXA [auth 2Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File