5TBW

Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides.

Konst, Z.A.Szklarski, A.R.Pellegrino, S.Michalak, S.E.Meyer, M.Zanette, C.Cencic, R.Nam, S.Voora, V.K.Horne, D.A.Pelletier, J.Mobley, D.L.Yusupova, G.Yusupov, M.Vanderwal, C.D.

(2017) Nat Chem 9: 1140-1149

  • DOI: https://doi.org/10.1038/nchem.2800
  • Primary Citation of Related Structures:  
    5TBW

  • PubMed Abstract: 

    The lissoclimides are unusual succinimide-containing labdane diterpenoids that were reported to be potent cytotoxins. Our short semisynthesis and analogue-oriented synthesis approaches provide a series of lissoclimide natural products and analogues that expand the structure-activity relationships (SARs) in this family. The semisynthesis approach yielded significant quantities of chlorolissoclimide (CL) to permit an evaluation against the National Cancer Institute's 60-cell line panel and allowed us to obtain an X-ray co-crystal structure of the synthetic secondary metabolite with the eukaryotic 80S ribosome. Although it shares a binding site with other imide-based natural product translation inhibitors, CL engages in a particularly interesting and novel face-on halogen-π interaction between the ligand's alkyl chloride and a guanine residue. Our analogue-oriented synthesis provides many more lissoclimide compounds, which were tested against aggressive human cancer cell lines and for protein synthesis inhibitory activity. Finally, computational modelling was used to explain the SARs of certain key compounds and set the stage for the structure-guided design of better translation inhibitors.


  • Organizational Affiliation

    Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, California 92697-2025, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth j],
WA [auth CD]
252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth k],
XA [auth CE]
386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AF [auth l],
YA [auth CF]
361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth m],
ZA [auth CG]
296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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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]
175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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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]
222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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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]
233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ADB [auth CK],
K [auth q]
191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10EB [auth CL],
L [auth r]
220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BFB [auth CM],
M [auth s]
169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AGB [auth CN],
N [auth t]
193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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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]
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AIB [auth CP],
P [auth v]
203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AJB [auth CQ],
Q [auth w]
197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AKB [auth CR],
R [auth x]
183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-ALB [auth CS],
S [auth y]
185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AMB [auth CT],
T [auth z]
188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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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 cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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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]
159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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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]
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AQB [auth CX],
X [auth 6]
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-ARB [auth CY],
Y [auth 7]
98Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25SB [auth CZ],
Z [auth 8]
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AAA [auth 9],
TB [auth DA]
126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ABA [auth AA],
UB [auth DB]
135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28CA [auth AB],
VB [auth DC]
148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth AC],
WB [auth DD]
58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EA [auth AD],
XB [auth DE]
97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AFA [auth AE],
YB [auth DF]
109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GA [auth AF],
ZB [auth DG]
127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AAC [auth DH],
HA [auth AG]
106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ABC [auth DI],
IA [auth AH]
112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ACC [auth DJ],
JA [auth AI]
119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ADC [auth DK],
KA [auth AJ]
99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AEC [auth DL],
LA [auth AK]
87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38FC [auth DM],
MA [auth AL]
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39GC [auth DN],
NA [auth AM]
50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40HC [auth DO],
OA [auth AN]
52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AIC [auth DP],
PA [auth AO]
25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AJC [auth DQ],
QA [auth AP]
105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AKC [auth DR],
RA [auth AQ]
91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor protein STM1SA [auth i]168Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1MPT4STO1YLR150WL9634.1
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0LC [auth p0]219Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor protein STM1MC [auth sM]104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1MPT4STO1YLR150WL9634.1
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AOC [auth B],
XD [auth s0]
206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-APC [auth C],
YD [auth s1]
216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2QC [auth D],
ZD [auth s2]
217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3AE [auth s3],
RC [auth E]
223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-ABE [auth s4],
SC [auth F]
260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5CE [auth s5],
TC [auth G]
206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-ADE [auth s6],
UC [auth H]
226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AEE [auth s7],
VC [auth I]
186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AFE [auth s8],
WC [auth J]
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AGE [auth s9],
XC [auth K]
185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AHE [auth c0],
YC [auth L]
105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AIE [auth c1],
ZC [auth M]
155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12AD [auth N],
JE [auth c2]
143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13BD [auth O],
KE [auth c3]
150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BCD [auth P],
LE [auth c4]
128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14BCRY2YJL191WJ0354
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15DD [auth Q],
ME [auth c5]
135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AED [auth R],
NE [auth c6]
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AFD [auth S]125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AGD [auth T],
PE [auth c8]
145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AHD [auth U],
QE [auth c9]
143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20ID [auth V],
RE [auth d0]
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AJD [auth W],
SE [auth d1]
87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AKD [auth X],
TE [auth d2]
129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ALD [auth Y],
UE [auth d3]
144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AMD [auth Z],
VE [auth d4]
134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
UniProt
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