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 

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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: https://doi.org/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. 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
MoleculeChains Sequence 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
MoleculeChains Sequence 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
MoleculeChains Sequence 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]178Haloarcula marismortuiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeH [auth F]120Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EI [auth G]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth H]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PK [auth I]145Haloarcula marismortuiMutation(s): 0 
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Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PL [auth J]132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PM [auth K]165Haloarcula marismortuiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eN [auth L]196Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PO [auth M]187Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eP [auth N]116Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19eQ [auth O]149Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eR [auth P]96Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PS [auth Q]155Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PT [auth R]85Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PU [auth S]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24eV [auth T]67Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PW [auth U]71Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PX [auth V]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChains Sequence 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
MoleculeChains Sequence 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37AeAA [auth Y]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eBA [auth Z]57Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eCA [auth 1]50Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44EDA [auth 2]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAB [auth 9]122Haloarcula marismortui
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Entity ID: 31
MoleculeChains LengthOrganismImage
5'-R(*CP*CP*AP*(PHE)*(ACA))-3'EA [auth 4]4Haloarcula marismortui
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
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
SR
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AH [auth 0]
AI [auth 0]
AJ [auth 0]
AK [auth 9]
BH [auth 0]
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
ACE
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YL [auth 4]ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
K
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MD [auth 0],
ND [auth 0]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
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AG [auth 0]
AL [auth L]
BG [auth 0]
BL [auth M]
CG [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
MG
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AB [auth 0]
AC [auth 0]
AD [auth 0]
BB [auth 0]
BC [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
NA
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AE [auth 0]
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SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-02-21
    Changes: Data collection