2F4V

30S ribosome + designer antibiotic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interactions of designer antibiotics and the bacterial ribosome aminoacyl-tRNA site

Murray, J.B.Meroueh, S.O.Russell, R.J.Lentzen, G.Haddad, J.Mobashery, S.

(2006) Chem Biol 13: 129-138

  • DOI: 10.1016/j.chembiol.2005.11.004
  • Primary Citation of Related Structures:  
    2F4V, 2F4U, 2F4T, 2F4S

  • PubMed Abstract: 
  • The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described ...

    The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.


    Organizational Affiliation

    Vernalis (R&D), Ltd., Granta Park, Cambridge, UK. j.murray@vernalis.com



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2C [auth B]256Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3D [auth C]239Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4E [auth D]209Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5F [auth E]162Thermus thermophilusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6G [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7H [auth G]156Thermus thermophilusMutation(s): 0 
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Entity ID: 9
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30S ribosomal protein S8I [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9J [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10K [auth J]105Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11L [auth K]129Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12M [auth L]132Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13N [auth M]126Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14O [auth N]61Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15P [auth O]89Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16Q [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17R [auth Q]105Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18S [auth R]88Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19T [auth S]93Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20U [auth T]106Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1511Thermus thermophilus
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(P*UP*UP*CP*U)-3'B [auth Z]4Thermus thermophilus
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    AB9
    Query on AB9

    Download Ideal Coordinates CCD File 
    CE [auth A](2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE
    C20 H43 N7 O8
    OGRDTONULPXNRP-HSDDYVLRSA-N
     Ligand Interaction
    D2C
    Query on D2C

    Download Ideal Coordinates CCD File 
    BE [auth A](2S,4S,4AR,5AS,6S,11R,11AS,12R,12AR)-7-CHLORO-4-(DIMETHYLAMINO)-6,10,11,12-TETRAHYDROXY-1,3-DIOXO-1,2,3,4,4A,5,5A,6,11,11A,12,12A-DODECAHYDROTETRACENE-2-CARBOXAMIDE
    C21 H25 Cl N2 O7
    DMSXRSJJYGANOR-VAVXRSHRSA-N
     Ligand Interaction
    ZN
    Query on ZN

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

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    AA [auth A] , IA [auth A] , KA [auth A] , OA [auth A] , PB [auth A] , PC [auth A] , PD [auth A] , SC [auth A] , 
    AA [auth A],  IA [auth A],  KA [auth A],  OA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  SC [auth A],  WA [auth A],  XA [auth A],  Z [auth A],  ZC [auth A]
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , BA [auth A] , BB [auth A] , BC [auth A] , BD [auth A] , 
    AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth Z],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth D],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth M],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  PA [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  SA [auth A],  SB [auth A],  SD [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  V [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  W [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  X [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  ZA [auth A],  ZB [auth A],  ZD [auth A]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.80 Å
    • R-Value Free: 0.315 
    • R-Value Work: 0.259 
    • R-Value Observed: 0.262 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 403.323α = 90
    b = 403.323β = 90
    c = 176.685γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2006-07-04
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance