3CPW

The structure of the antibiotic LINEZOLID bound to the large ribosomal subunit of HALOARCULA MARISMORTUI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit

Ippolito, J.A.Kanyo, Z.K.Wang, D.Franceschi, F.J.Moore, P.B.Steitz, T.A.Duffy, E.M.

(2008) J Med Chem 51: 3353-3356

  • DOI: 10.1021/jm800379d
  • Primary Citation of Related Structures:  
    3CPW

  • PubMed Abstract: 
  • The oxazolidinone antibacterials target the 50S subunit of prokaryotic ribosomes. To gain insight into their mechanism of action, the crystal structure of the canonical oxazolidinone, linezolid, has been determined bound to the Haloarcula marismortui 50S subunit ...

    The oxazolidinone antibacterials target the 50S subunit of prokaryotic ribosomes. To gain insight into their mechanism of action, the crystal structure of the canonical oxazolidinone, linezolid, has been determined bound to the Haloarcula marismortui 50S subunit. Linezolid binds the 50S A-site, near the catalytic center, which suggests that inhibition involves competition with incoming A-site substrates. These results provide a structural basis for the discovery of improved oxazolidinones active against emerging drug-resistant clinical strains.


    Organizational Affiliation

    Department of Structure-Based Drug Design, Rib-X Pharmaceuticals Inc, 300 George Street, Suite 301, New Haven, CT 06511, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2PC [auth A]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3PD [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4PE [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]178Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeH [auth F]120Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10EI [auth G]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth H]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13PK [auth I]145Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14PL [auth J]132Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 13
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50S ribosomal protein L15PM [auth K]165Haloarcula marismortuiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15eN [auth L]196Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18PO [auth M]187Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18eP [auth N]116Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19eQ [auth O]149Haloarcula marismortuiMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21eR [auth P]96Haloarcula marismortuiMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L22PS [auth Q]155Haloarcula marismortuiMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PT [auth R]85Haloarcula marismortuiMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24PU [auth S]120Haloarcula marismortuiMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24eV [auth T]67Haloarcula marismortuiMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29PW [auth U]71Haloarcula marismortuiMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PX [auth V]154Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31eY [auth W]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32eZ [auth X]241Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37AeAA [auth Y]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37eBA [auth Z]57Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39eCA [auth 1]50Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44EDA [auth 2]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAA [auth 0]2922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAB [auth 9]122Haloarcula marismortui
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  • Entity ID: 31
    MoleculeChainsLengthOrganismImage
    5'-R(*CP*CP*AP*(PHE)*(ACA))-3'EA [auth 4]4Haloarcula marismortui
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 8 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZLD
    Query on ZLD

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    FA [auth 0]N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide
    C16 H20 F N3 O4
    TYZROVQLWOKYKF-ZDUSSCGKSA-N
     Ligand Interaction
    CD
    Query on CD

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    CL [auth N], NL [auth T], QL [auth Y], RL [auth Z], VL [auth 2]CADMIUM ION
    Cd
    WLZRMCYVCSSEQC-UHFFFAOYSA-N
     Ligand Interaction
    SR
    Query on SR

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    AH [auth 0] , AI [auth 0] , AJ [auth 0] , AK [auth 9] , BH [auth 0] , BI [auth 0] , BJ [auth 0] , BK [auth 9] , 
    AH [auth 0],  AI [auth 0],  AJ [auth 0],  AK [auth 9],  BH [auth 0],  BI [auth 0],  BJ [auth 0],  BK [auth 9],  CH [auth 0],  CI [auth 0],  CJ [auth 0],  CK [auth 9],  DH [auth 0],  DI [auth 0],  DJ [auth 0],  EH [auth 0],  EI [auth 0],  EJ [auth 0],  FH [auth 0],  FI [auth 0],  FJ [auth 0],  GH [auth 0],  GI [auth 0],  GJ [auth 0],  GK [auth A],  HH [auth 0],  HI [auth 0],  HJ [auth 0],  HK [auth A],  IH [auth 0],  II [auth 0],  IJ [auth 0],  IK [auth A],  IL [auth Q],  JG [auth 0],  JH [auth 0],  JI [auth 0],  JJ [auth 0],  KG [auth 0],  KH [auth 0],  KI [auth 0],  KJ [auth 0],  KL [auth R],  LG [auth 0],  LH [auth 0],  LI [auth 0],  LJ [auth 0],  MG [auth 0],  MH [auth 0],  MI [auth 0],  MJ [auth 0],  MK [auth B],  ML [auth S],  NG [auth 0],  NH [auth 0],  NI [auth 0],  NJ [auth 0],  NK [auth B],  OG [auth 0],  OH [auth 0],  OI [auth 0],  OJ [auth 0],  PG [auth 0],  PH [auth 0],  PI [auth 0],  PJ [auth 0],  PK [auth F],  QG [auth 0],  QH [auth 0],  QI [auth 0],  QJ [auth 0],  QK [auth H],  RG [auth 0],  RH [auth 0],  RI [auth 0],  RJ [auth 0],  SG [auth 0],  SH [auth 0],  SI [auth 0],  SJ [auth 0],  SL [auth Z],  TG [auth 0],  TH [auth 0],  TI [auth 0],  TJ [auth 0],  TL [auth Z],  UG [auth 0],  UH [auth 0],  UI [auth 0],  UJ [auth 0],  VG [auth 0],  VH [auth 0],  VI [auth 0],  VJ [auth 0],  WG [auth 0],  WH [auth 0],  WI [auth 0],  WJ [auth 0],  XG [auth 0],  XH [auth 0],  XI [auth 0],  XL [auth 2],  YG [auth 0],  YH [auth 0],  YI [auth 0],  ZG [auth 0],  ZH [auth 0],  ZI [auth 0]
    STRONTIUM ION
    Sr
    PWYYWQHXAPXYMF-UHFFFAOYSA-N
     Ligand Interaction
    ACE
    Query on ACE

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    YL [auth 4]ACETYL GROUP
    C2 H4 O
    IKHGUXGNUITLKF-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

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    MD [auth 0], ND [auth 0]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

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    AG [auth 0] , AL [auth L] , BG [auth 0] , BL [auth M] , CG [auth 0] , DG [auth 0] , DL [auth N] , EG [auth 0] , 
    AG [auth 0],  AL [auth L],  BG [auth 0],  BL [auth M],  CG [auth 0],  DG [auth 0],  DL [auth N],  EG [auth 0],  FG [auth 0],  FK [auth A],  GG [auth 0],  HG [auth 0],  HL [auth Q],  IG [auth 0],  LK [auth B],  PL [auth X],  SK [auth I],  TK [auth I],  UK [auth I],  WK [auth J],  WL [auth 2],  YK [auth K]
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

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    AB [auth 0] , AC [auth 0] , AD [auth 0] , BB [auth 0] , BC [auth 0] , BD [auth 0] , CB [auth 0] , CC [auth 0] , 
    AB [auth 0],  AC [auth 0],  AD [auth 0],  BB [auth 0],  BC [auth 0],  BD [auth 0],  CB [auth 0],  CC [auth 0],  CD [auth 0],  DB [auth 0],  DC [auth 0],  DD [auth 0],  DK [auth A],  EB [auth 0],  EC [auth 0],  ED [auth 0],  EK [auth A],  FB [auth 0],  FC [auth 0],  FD [auth 0],  GA [auth 0],  GB [auth 0],  GC [auth 0],  GD [auth 0],  HA [auth 0],  HB [auth 0],  HC [auth 0],  HD [auth 0],  IA [auth 0],  IB [auth 0],  IC [auth 0],  ID [auth 0],  JA [auth 0],  JB [auth 0],  JC [auth 0],  JD [auth 0],  JK [auth B],  KA [auth 0],  KB [auth 0],  KC [auth 0],  KD [auth 0],  LA [auth 0],  LB [auth 0],  LC [auth 0],  LD [auth 0],  LL [auth S],  MA [auth 0],  MB [auth 0],  MC [auth 0],  NA [auth 0],  NB [auth 0],  NC [auth 0],  OA [auth 0],  OB [auth 0],  OC [auth 0],  OL [auth X],  PA [auth 0],  PB [auth 0],  PC [auth 0],  QA [auth 0],  QB [auth 0],  QC [auth 0],  RA [auth 0],  RB [auth 0],  RC [auth 0],  SA [auth 0],  SB [auth 0],  SC [auth 0],  TA [auth 0],  TB [auth 0],  TC [auth 0],  UA [auth 0],  UB [auth 0],  UC [auth 0],  UL [auth 1],  VA [auth 0],  VB [auth 0],  VC [auth 0],  VK [auth J],  WA [auth 0],  WB [auth 0],  WC [auth 0],  XA [auth 0],  XB [auth 0],  XC [auth 0],  XJ [auth 9],  YA [auth 0],  YB [auth 0],  YC [auth 0],  ZA [auth 0],  ZB [auth 0],  ZC [auth 0]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

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    AE [auth 0] , AF [auth 0] , BE [auth 0] , BF [auth 0] , CE [auth 0] , CF [auth 0] , DE [auth 0] , DF [auth 0] , 
    AE [auth 0],  AF [auth 0],  BE [auth 0],  BF [auth 0],  CE [auth 0],  CF [auth 0],  DE [auth 0],  DF [auth 0],  EE [auth 0],  EF [auth 0],  EL [auth P],  FE [auth 0],  FF [auth 0],  FL [auth Q],  GE [auth 0],  GF [auth 0],  GL [auth Q],  HE [auth 0],  HF [auth 0],  IE [auth 0],  IF [auth 0],  JE [auth 0],  JF [auth 0],  JL [auth R],  KE [auth 0],  KF [auth 0],  KK [auth B],  LE [auth 0],  LF [auth 0],  ME [auth 0],  MF [auth 0],  NE [auth 0],  NF [auth 0],  OD [auth 0],  OE [auth 0],  OF [auth 0],  OK [auth C],  PD [auth 0],  PE [auth 0],  PF [auth 0],  QD [auth 0],  QE [auth 0],  QF [auth 0],  RD [auth 0],  RE [auth 0],  RF [auth 0],  RK [auth I],  SD [auth 0],  SE [auth 0],  SF [auth 0],  TD [auth 0],  TE [auth 0],  TF [auth 0],  UD [auth 0],  UE [auth 0],  UF [auth 0],  VD [auth 0],  VE [auth 0],  VF [auth 0],  WD [auth 0],  WE [auth 0],  WF [auth 0],  XD [auth 0],  XE [auth 0],  XF [auth 0],  XK [auth K],  YD [auth 0],  YE [auth 0],  YF [auth 0],  YJ [auth 9],  ZD [auth 0],  ZE [auth 0],  ZF [auth 0],  ZJ [auth 9],  ZK [auth L]
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.230 
    • R-Value Work: 0.191 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 211.73α = 90
    b = 298.58β = 90
    c = 575.29γ = 90
    Software Package:
    Software NamePurpose
    CNXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    CNXphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2008-07-22
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2015-03-11
      Changes: Structure summary
    • Version 1.3: 2015-07-22
      Changes: Non-polymer description
    • Version 1.4: 2018-04-25
      Changes: Advisory, Data collection, Derived calculations, Source and taxonomy