7PZY

Structure of the vacant Candida albicans 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

E-site drug specificity of the human pathogen Candida albicans ribosome.

Zgadzay, Y.Kolosova, O.Stetsenko, A.Wu, C.Bruchlen, D.Usachev, K.Validov, S.Jenner, L.Rogachev, A.Yusupova, G.Sachs, M.S.Guskov, A.Yusupov, M.

(2022) Sci Adv 8: eabn1062-eabn1062

  • DOI: 10.1126/sciadv.abn1062
  • Primary Citation of Related Structures:  
    7PZY, 7Q08, 7Q0F, 7Q0P, 7Q0R

  • PubMed Abstract: 
  • Candida albicans is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds to the E-transfer RNA binding site of the ribosome ...

    Candida albicans is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds to the E-transfer RNA binding site of the ribosome. Because of lack of structural information, it is neither possible to understand the nature of the resistance nor to develop novel inhibitors. To overcome this issue, we determined the structure of the vacant C. albicans 80 S ribosome at 2.3 angstroms and its complexes with bound inhibitors at resolutions better than 2.9 angstroms using cryo-electron microscopy. Our structures reveal how a change in a conserved amino acid in ribosomal protein eL42 explains CHX resistance in C. albicans and forms a basis for further antifungal drug development.


    Organizational Affiliation

    Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan, Russia.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L2AE [auth j]254Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL2orf19.2309.2CAALFM_C111060CA
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth k]389Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL3orf19.9169CAALFM_C209430WA
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L4BG [auth l]363Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL4Borf19.7217CAALFM_C114110CA
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L5H [auth m]298Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL5orf19.13894CAALFM_C701790CA
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth n]176Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL6orf19.3003.1CAALFM_C103110WA
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L7AJ [auth o]241Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.2478.1CAALFM_C105720WA
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8K [auth p]262Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL8Borf19.13423CAALFM_C305240CA
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L9BL [auth q]191Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL9Borf19.7866CAALFM_C302470CA
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L10M [auth r]220Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL10orf19.10452CAALFM_C102460WA
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L11BN [auth s]174Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL11orf19.9774CAALFM_C206810CA
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13O [auth t]202Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL13CAALFM_C103020CACa49C10.02CaO19.10511CaO19.2994
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L14BP [auth u]131Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL14orf19.4931.1CAALFM_C113050WA
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth v]204Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL15ACAALFM_CR04100CAorf19.8123
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L16AR [auth w]200Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL16Aorf19.13504CAALFM_C100180WA
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L17BS [auth x]185Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL17Borf19.11966CAALFM_C204600CA
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Find proteins for Q59TE0 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 20
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Ribosomal 60S subunit protein L18AT [auth y]186Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL18orf19.13403CAALFM_C305100CA
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Find proteins for A0A1D8PK43 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L19U [auth z]190Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL19Aorf19.13325CAALFM_C304500CA
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Find proteins for A0A1D8PK40 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20V [auth 0]172Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL20Borf19.12102CAALFM_C401520CA
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L21AW [auth 2]160Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL21Aorf19.8460CAALFM_C203810CA
UniProt
Find proteins for A0A1D8PGY0 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L22BX [auth 5]124Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.1409.1CAALFM_C404390WA
UniProt
Find proteins for A0A1D8PM41 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L23BY [auth 6]137Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL23Aorf19.10998CAALFM_C602070CA
UniProt
Find proteins for A0A1D8PPT5 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L24AZ [auth 7]155Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL24Aorf19.3789CAALFM_C404890CA
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L25AA [auth 8]142Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL25orf19.687.1CAALFM_C601970CA
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Entity ID: 28
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Ribosomal 60S subunit protein L26BBA [auth 9]127Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.3690.2CAALFM_C102330CA
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth AA]136Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL27ACAALFM_C112390CA
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L28DA [auth AB]149Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL28CAALFM_CR03030CAorf19.2425.2
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Entity ID: 31
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60S ribosomal protein L29EA [auth AC]63Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL29orf19.2310.1CAALFM_C111040WA
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L30FA [auth AD]106Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL30orf19.3788.1CAALFM_C404900WA
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L31BGA [auth AE]112Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.3572.3CAALFM_C205410WA
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Entity ID: 34
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Ribosomal 60S subunit protein L32HA [auth AF]131Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL32CAALFM_C601700WA
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Entity ID: 35
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Ribosomal 60S subunit protein L33AIA [auth AG]107Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.6882.1CAALFM_C205710CA
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Entity ID: 36
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Ribosomal 60S subunit protein L34BJA [auth AH]122Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.6220.4CAALFM_C106890CA
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Entity ID: 37
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Ribosomal 60S subunit protein L35AKA [auth AI]120Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL35orf19.5964.2CAALFM_C304960WA
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Entity ID: 38
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60S ribosomal protein L36LA [auth AJ]99Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL39CAALFM_C203960WA
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Entity ID: 39
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Ribosomal protein L37MA [auth AK]90Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL37Borf19.667.1CAALFM_C111360WA
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Entity ID: 40
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Ribosomal 60S subunit protein L38NA [auth AL]78Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL38orf19.2111.2CAALFM_C200210WA
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Find proteins for A0A1D8PG16 (Candida albicans (strain SC5314 / ATCC MYA-2876))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39OA [auth AM]51Candida albicans SC5314Mutation(s): 0 
Gene Names: CAALFM_C106470WA
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Rpl40bpPA [auth AN]52Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL40Borf19.4684.2CAALFM_C401050CA
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41QA [auth AO]25Candida albicans SC5314Mutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L42ARA [auth AP]106Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL42orf19.4909.1CAALFM_C110390CA
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal 60S subunit protein L43ASA [auth AQ]92Candida albicans SC5314Mutation(s): 0 
Gene Names: RPL43Aorf19.3942.1CAALFM_C504590CA
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Entity ID: 46
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HABP4_PAI-RBP1 domain-containing proteinTA [auth i]267Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.5943.1CAALFM_C304810CA
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0VA [auth B]261Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS0YST1CAALFM_C305370CACaO19.6975
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Entity ID: 49
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40S ribosomal protein S1WA [auth C]256Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS1PLC1RP10RPS10CAALFM_C103090WACaO19.10520CaO19.3002
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Entity ID: 50
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Ribosomal 40S subunit protein S2XA [auth D]249Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS21orf19.10845CAALFM_C101480CA
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Entity ID: 51
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Ribosomal 40S subunit protein S3YA [auth E]251Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS3CAALFM_CR04810WAorf19.13689
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Entity ID: 52
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40S ribosomal protein S4ZA [auth F]262Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS42orf19.10862CAALFM_C101640WA
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Entity ID: 53
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Ribosomal 40S subunit protein S5AB [auth G]225Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS5orf19.11812CAALFM_C503070WA
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Entity ID: 54
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40S ribosomal protein S6BB [auth H]236Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS6Aorf19.12130CAALFM_C401270WA
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Entity ID: 55
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40S ribosomal protein S7CB [auth I]186Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS7Aorf19.9267CAALFM_C301490WA
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Entity ID: 56
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40S ribosomal protein S8DB [auth J]206Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS8Aorf19.14162CAALFM_C205610CA
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Entity ID: 57
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Ribosomal 40S subunit protein S9BEB [auth K]189Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS9Borf19.838.1CAALFM_C203820CA
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Entity ID: 58
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Ribosomal 40S subunit protein S10AFB [auth L]118Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS10orf19.2179.2CAALFM_C208040CA
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Entity ID: 59
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Ribosomal 40S subunit protein S11AGB [auth M]155Candida albicans SC5314Mutation(s): 0 
Gene Names: orf19.4149.1CAALFM_C501540WA
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Entity ID: 60
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40S ribosomal protein S12HB [auth N]143Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS12orf19.14077CAALFM_C307150CA
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Entity ID: 61
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Ribosomal 40S subunit protein S13IB [auth O]151Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS13orf19.4193.1CAALFM_C600650CA
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Entity ID: 62
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Ribosomal 40S subunit protein S14BJB [auth P]132Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS14Borf19.6265.1CAALFM_C106450CA
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Entity ID: 63
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Ribosomal 40S subunit protein S15KB [auth Q]142Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS15orf19.13348CAALFM_C304670CA
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Entity ID: 64
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Ribosomal 40S subunit protein S16ALB [auth R]142Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS16ACAALFM_C103030WA
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Entity ID: 65
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Ribosomal 40S subunit protein S17BMB [auth S]137Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS17Borf19.2329.1CAALFM_C110870WA
UniProt
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Entity ID: 66
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Ribosomal 40S subunit protein S18BNB [auth T]145Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS18orf19.7018CAALFM_C700960WA
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Entity ID: 67
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Ribosomal 40S subunit protein S19AOB [auth U]145Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS19Aorf19.5996.1CAALFM_C305200WA
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Entity ID: 68
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Ribosomal 40S subunit protein S20PB [auth V]119Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS20CAALFM_CR08150WAorf19.13732
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Entity ID: 69
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40S ribosomal protein S21QB [auth W]87Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS21BCAALFM_C101370CA
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Entity ID: 70
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40S ribosomal protein S22-ARB [auth X]130Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS22ARPS22CAALFM_C106460CACaO19.13644CaO19.6265
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Entity ID: 71
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Ribosomal 40S subunit protein S23BSB [auth Y]145Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS23Aorf19.13632CAALFM_C106580WA
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Entity ID: 72
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40S ribosomal protein S24TB [auth Z]135Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS24orf19.12921CAALFM_C300090WA
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Entity ID: 73
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40S ribosomal protein S25UB [auth a]105Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS25Borf19.6663CAALFM_C503540CA
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Entity ID: 74
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40S ribosomal protein S26VB [auth b]119Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS26Aorf19.9045CAALFM_C201610CA
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Entity ID: 75
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40S ribosomal protein S27WB [auth c]82Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS27CAALFM_CR07630CAorf19.6286.2
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Entity ID: 76
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Ribosomal 40S subunit protein S28BXB [auth d]67Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS28Borf19.7048.1CAALFM_C700710WA
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Entity ID: 77
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Ribosomal 40S subunit protein S29AYB [auth e]56Candida albicans SC5314Mutation(s): 0 
Gene Names: CAALFM_CR08480CAorf19.6415.1
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Entity ID: 78
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40S ribosomal protein S30ZB [auth f]63Candida albicans SC5314Mutation(s): 0 
Gene Names: RPS30CAALFM_CR03770CAorf19.4375.1
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Entity ID: 79
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Ubiquitin-ribosomal 40S subunit protein S31 fusion proteinAC [auth g]193Candida albicans SC5314Mutation(s): 0 
Gene Names: UBI3orf19.10599CAALFM_C407180WA
UniProt
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Entity ID: 80
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Guanine nucleotide-binding protein subunit beta-like proteinBC [auth h]317Candida albicans SC5314Mutation(s): 0 
Gene Names: ASC1CAALFM_C701250WACaJ7.0140CaO19.6906
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S ribosomal RNAA [auth 1]3,359Candida albicans SC5314
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 3]121Candida albicans SC5314
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAC [auth 4]158Candida albicans SC5314
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Entity ID: 4
MoleculeChainsLengthOrganismImage
Mixture of endogenous E-tRNAsD [auth 10]76Candida albicans SC5314
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Entity ID: 47
MoleculeChainsLengthOrganismImage
18S ribosomal RNAUA [auth A]1,787Candida albicans SC5314
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

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CC [auth 1],
DC [auth 1],
FC [auth 1],
GC [auth 1],
HC [auth 1],
CC [auth 1],
DC [auth 1],
FC [auth 1],
GC [auth 1],
HC [auth 1],
IC [auth 1],
JC [auth 1],
KC [auth 1],
LC [auth 1],
MC [auth 1]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

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EC [auth 1],
XN [auth 4]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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IO [auth AK],
KO [auth AN],
LO [auth AP],
NO [auth AQ],
TT [auth b],
IO [auth AK],
KO [auth AN],
LO [auth AP],
NO [auth AQ],
TT [auth b],
UT [auth c],
VT [auth e],
WT [auth g]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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