6HHQ

Crystal structure of compound C45 bound to the yeast 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome.

Pellegrino, S.Meyer, M.Konst, Z.A.Holm, M.Voora, V.K.Kashinskaya, D.Zanette, C.Mobley, D.L.Yusupova, G.Vanderwal, C.D.Blanchard, S.C.Yusupov, M.

(2019) Nucleic Acids Res 47: 3223-3232

  • DOI: https://doi.org/10.1093/nar/gkz053
  • Primary Citation of Related Structures:  
    6HHQ

  • PubMed Abstract: 

    Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity. Toward this goal, we have previously established a short synthesis pathway that grants access to multiple congeners of the lissoclimide family. Here we present the X-ray co-crystal structure at 3.1 Å resolution of C45, a potent congener with two A-ring chlorine-bearing stereogenic centers with 'unnatural' configurations, with the yeast 80S ribosome, intermolecular interaction energies of the C45/ribosome complex, and single-molecule FRET data quantifying the impact of C45 on both human and yeast ribosomes. Together, these data provide new insights into the role of unusual non-covalent halogen bonding interactions involved in the binding of this synthetic compound to the 80S ribosome.


  • Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth j],
WA [auth CD]
254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth k],
XA [auth CE]
387Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AF [auth l],
YA [auth CF]
362Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth m],
ZA [auth CG]
297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AAB [auth CH],
H [auth n]
176Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ABB [auth CI],
I [auth o]
244Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-ACB [auth CJ],
J [auth p]
256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ADB [auth CK],
K [auth q]
191Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10EB [auth CL],
L [auth r]
221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BFB [auth CM],
M [auth s]
174Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AGB [auth CN],
N [auth t]
199Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AHB [auth CO],
O [auth u]
138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AIB [auth CP],
P [auth v]
204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AJB [auth CQ],
Q [auth w]
199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AKB [auth CR],
R [auth x]
184Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-ALB [auth CS],
S [auth y]
186Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AMB [auth CT],
T [auth z]
189Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-ANB [auth CU],
U [auth 0]
172Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AOB [auth CV],
V [auth 2]
160Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-APB [auth CW],
W [auth 5]
121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AQB [auth CX],
X [auth 6]
137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-ARB [auth CY],
Y [auth 7]
155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25SB [auth CZ],
Z [auth 8]
142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AAA [auth 9],
TB [auth DA]
127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ABA [auth AA],
UB [auth DB]
136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28CA [auth AB],
VB [auth DC]
149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth AC],
WB [auth DD]
59Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EA [auth AD],
XB [auth DE]
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AFA [auth AE],
YB [auth DF]
113Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GA [auth AF],
ZB [auth DG]
130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AAC [auth DH],
HA [auth AG]
107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ABC [auth DI],
IA [auth AH]
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ACC [auth DJ],
JA [auth AI]
120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ADC [auth DK],
KA [auth AJ]
100Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AEC [auth DL],
LA [auth AK]
88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38FC [auth DM],
MA [auth AL]
78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39GC [auth DN],
NA [auth AM]
51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40HC [auth DO],
OA [auth AN]
128Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-BIC [auth DP],
PA [auth AO]
25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AJC [auth DQ],
QA [auth AP]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AKC [auth DR],
RA [auth AQ]
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor protein STM1MC [auth sM],
SA [auth i]
273Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0LC [auth p0]312Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AOC [auth B],
XD [auth s0]
252Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-APC [auth C],
YD [auth s1]
255Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2QC [auth D],
ZD [auth s2]
254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3AE [auth s3],
RC [auth E]
240Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-ABE [auth s4],
SC [auth F]
261Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5CE [auth s5],
TC [auth G]
225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-ADE [auth s6],
UC [auth H]
236Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AEE [auth s7],
VC [auth I]
190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AFE [auth s8],
WC [auth J]
200Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AGE [auth s9],
XC [auth K]
197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AHE [auth c0],
YC [auth L]
105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AIE [auth c1],
ZC [auth M]
156Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12AD [auth N],
JE [auth c2]
143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13BD [auth O],
KE [auth c3]
151Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BCD [auth P],
LE [auth c4]
138Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15DD [auth Q],
ME [auth c5]
142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AED [auth R],
NE [auth c6]
143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AFD [auth S],
OE [auth c7]
136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AGD [auth T],
PE [auth c8]
146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AHD [auth U],
QE [auth c9]
144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20ID [auth V],
RE [auth d0]
121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AJD [auth W],
SE [auth d1]
87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AKD [auth X],
TE [auth d2]
130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ALD [auth Y],
UE [auth d3]
145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AMD [auth Z],
VE [auth d4]
135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AND [auth a],
WE [auth d5]
108Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-BOD [auth b],
XE [auth d6]
119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-APD [auth c],
YE [auth d7]
82Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AQD [auth d],
ZE [auth d8]
67Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AAF [auth d9],
RD [auth e]
56Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-ABF [auth e0],
SD [auth f]
63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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