5TCU

Methicillin sensitive Staphylococcus aureus 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome.

Belousoff, M.J.Eyal, Z.Radjainia, M.Ahmed, T.Bamert, R.S.Matzov, D.Bashan, A.Zimmerman, E.Mishra, S.Cameron, D.Elmlund, H.Peleg, A.Y.Bhushan, S.Lithgow, T.Yonath, A.

(2017) mBio 8

  • DOI: 10.1128/mBio.00395-17
  • Primary Citation of Related Structures:  
    5T7V, 5TCU

  • PubMed Abstract: 
  • An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural informatio ...

    An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel trevor.lithgow@monash.edu ada.yonath@weizmann.ac.il.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3SB202Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsCSAOUHSC_02506
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4SC198Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsDSAOUHSC_01829
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5SD156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsESAOUHSC_02494
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6SE95Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsFSAOUHSC_00348
Find proteins for Q2G113 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7SG155Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsGSAOUHSC_00528
Find proteins for P48940 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8SF130Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsHSAOUHSC_02498
Find proteins for Q2FW20 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9SH127Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsISAOUHSC_02477
Find proteins for Q2FW39 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10S180Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Find proteins for Q2YYP5 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11S2114Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsKSAOUHSC_02486
Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12S3136Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsLSAOUHSC_00527
Find proteins for P0A0H0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13S4113Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsMSAOUHSC_02487
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZS560Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsZrpsN1SAOUHSC_02499
Find proteins for Q2FW19 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15S688Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsOSAOUHSC_01250
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16S783Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsPSAOUHSC_01208
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17S880Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsQSAOUHSC_02503
Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18S956Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsRSAOUHSC_00350
Find proteins for Q2G111 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19SI78Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsSSAOUHSC_02508
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20SA79Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsTSAOUHSC_01689
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2L2274Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3LC215Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4LJ205Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5LK166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6LL174Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13LM145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14LN122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15LO145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16LP136Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17LQ119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18LR113Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19L1109Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20L3116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21L4102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 39
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50S ribosomal protein L22L5112Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23L689Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24L7103Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25L893Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplYctcSAOUHSC_00474
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 43
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50S ribosomal protein L27L982Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28LA58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmBSAOUHSC_01191
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 45
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50S ribosomal protein L29LB62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 46
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50S ribosomal protein L30LD57Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32LE47Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 1LS47Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmG1SAOUHSC_01328
Find proteins for Q2FYU6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34LG43Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35LH60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36LI37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmJSAOUHSC_02488
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BLF74Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmE2SAOUHSC_02361
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAA1555Staphylococcus aureus subsp. aureus NCTC 8325
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  • Entity ID: 20
    MoleculeChainsLengthOrganismImage
    mRNAX13Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 21
    MoleculeChainsLengthOrganismImage
    P-site tRNA CHAINE75Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 22
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    E-site tRNA CHAIND76Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 23
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    23S RRNAB2923Staphylococcus aureus subsp. aureus NCTC 8325
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    Entity ID: 24
    MoleculeChainsLengthOrganismImage
    5S rRNA CHAINC114Staphylococcus aureus subsp. aureus NCTC 8325
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PAR
    Query on PAR

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    A
    PAROMOMYCIN
    C23 H45 N5 O14
    UOZODPSAJZTQNH-LSWIJEOBSA-N
     Ligand Interaction
    MG
    Query on MG

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    A, B, C, SG
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Health and Medical Research Council (NHMRC, Australia)Australia1092262
    European Research Council (ERC)European Union322581 (NOVRIB)

    Revision History 

    • Version 1.0: 2017-05-24
      Type: Initial release
    • Version 1.1: 2017-09-20
      Changes: Author supporting evidence, Data collection
    • Version 1.2: 2019-12-18
      Changes: Advisory, Author supporting evidence, Derived calculations, Other