4B3R

Crystal structure of the 30S ribosome in complex with compound 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics

Perez-Fernandez, D.Shcherbakov, D.Matt, T.Leong, N.C.Kudyba, I.Duscha, S.Boukari, H.Patak, R.Dubakka, S.R.Lang, K.Meyer, M.Akbergenov, R.Freihofer, P.Vaddi, S.Thommes, P.Ramakrishnan, V.Vasella, A.Bottger, E.C.

(2014) Nat Commun 5: 3112

  • DOI: 10.1038/ncomms4112
  • Primary Citation of Related Structures:  
    4B3M, 4B3R, 4B3S, 4B3T

  • PubMed Abstract: 
  • Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides ...

    Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.


    Organizational Affiliation

    Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80371 
Go to UniProtKB:  P80371
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80372 
Go to UniProtKB:  P80372
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80373 
Go to UniProtKB:  P80373
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E161Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHQ5 
Go to UniProtKB:  Q5SHQ5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SLP8 
Go to UniProtKB:  Q5SLP8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P17291 
Go to UniProtKB:  P17291
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P0DOY9 
Go to UniProtKB:  P0DOY9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80374 
Go to UniProtKB:  P80374
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHN7 
Go to UniProtKB:  Q5SHN7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80376 
Go to UniProtKB:  P80376
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHN3 
Go to UniProtKB:  Q5SHN3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80377 
Go to UniProtKB:  P80377
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE ZN60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P0DOY6 
Go to UniProtKB:  P0DOY6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SJ76 
Go to UniProtKB:  Q5SJ76
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SJH3 
Go to UniProtKB:  Q5SJH3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P0DOY7 
Go to UniProtKB:  P0DOY7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SLQ0 
Go to UniProtKB:  Q5SLQ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S92Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHP2 
Go to UniProtKB:  Q5SHP2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80380 
Go to UniProtKB:  P80380
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXU [auth V]26Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SIH3 
Go to UniProtKB:  Q5SIH3
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1521Thermus thermophilus HB8
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*UP*CP*AP*AP*AP)-3'V [auth W]6Thermus thermophilus HB8
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP-3'W [auth Z]16Thermus thermophilus HB8
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      M5Z
      Query on M5Z

      Download Ideal Coordinates CCD File 
      DH [auth A](1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-4,6-O-[(1R)-3-phenylpropylidene]-alpha-D-glucopyranoside
      C32 H53 N5 O14
      JVOSAEIJIXVWJU-TZWNKDFKSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      JI [auth N], YH [auth D]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

      Download Ideal Coordinates CCD File 
      AF [auth A] , NE [auth A] , OE [auth A] , PE [auth A] , QE [auth A] , RE [auth A] , SE [auth A] , TE [auth A] , 
      AF [auth A],  NE [auth A],  OE [auth A],  PE [auth A],  QE [auth A],  RE [auth A],  SE [auth A],  TE [auth A],  UE [auth A],  VE [auth A],  WE [auth A],  XE [auth A],  YE [auth A],  ZE [auth A]
      POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AG [auth A] , AH [auth A] , AI [auth E] , 
      AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AG [auth A],  AH [auth A],  AI [auth E],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  BI [auth E],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth A],  CI [auth F],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  DI [auth H],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth A],  EI [auth H],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth A],  FI [auth J],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth A],  GI [auth K],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth A],  HI [auth L],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth A],  II [auth M],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  JH [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  KH [auth A],  KI [auth N],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth A],  LI [auth Q],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  MH [auth A],  MI [auth Q],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NF [auth A],  NG [auth A],  NH [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OF [auth A],  OG [auth A],  OH [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PF [auth A],  PG [auth A],  PH [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QF [auth A],  QG [auth A],  QH [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RF [auth A],  RG [auth A],  RH [auth A],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SF [auth A],  SG [auth A],  SH [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TF [auth A],  TG [auth A],  TH [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UF [auth A],  UG [auth A],  UH [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VF [auth A],  VG [auth A],  VH [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WF [auth A],  WG [auth A],  WH [auth B],  X [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XF [auth A],  XG [auth A],  XH [auth B],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YF [auth A],  YG [auth A],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZF [auth A],  ZG [auth A],  ZH [auth D]
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.248 
      • R-Value Work: 0.214 
      • R-Value Observed: 0.214 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 402.48α = 90
      b = 402.48β = 90
      c = 174.98γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      XDSdata reduction
      XSCALEdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Revision History  (Full details and data files)

      • Version 1.0: 2013-08-07
        Type: Initial release
      • Version 1.1: 2013-11-06
        Changes: Other, Structure summary
      • Version 1.2: 2013-12-11
        Changes: Other, Structure summary
      • Version 1.3: 2014-01-29
        Changes: Database references
      • Version 1.4: 2014-02-12
        Changes: Database references
      • Version 1.5: 2019-01-30
        Changes: Data collection, Experimental preparation, Other
      • Version 1.6: 2019-03-06
        Changes: Data collection, Experimental preparation
      • Version 1.7: 2019-05-22
        Changes: Data collection, Refinement description