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
  • Structures With Same Primary Citation

  • 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 LengthOrganismDetails
50S ribosomal protein L2PA240Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P20276
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3PB338Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4PC246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5PD177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6PE178Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7AeF120Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10EG348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10eH177Haloarcula marismortuiMutation(s): 0 
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13PI145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14PJ132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15PK165Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15eL196Haloarcula marismortuiMutation(s): 0 
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18PM187Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18eN116Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12733
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19eO149Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21eP96Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22PQ155Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23PR85Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24PS120Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P10972
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24eT67Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14116
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29PU71Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P10971
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30PV154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14121
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31eW92Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P18138
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32eX241Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12736
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AeY92Haloarcula marismortuiMutation(s): 0 
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P60619
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37eZ57Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P32410 
Go to UniProtKB:  P32410
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e150Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P22452 
Go to UniProtKB:  P22452
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E292Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P32411 
Go to UniProtKB:  P32411
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02922Haloarcula marismortui

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Entity ID: 2
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA9122Haloarcula marismortui
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Entity ID: 31
MoleculeChainsLengthOrganism
5'-R(*CP*CP*AP*(PHE)*(ACA))-3'44Haloarcula marismortui
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZLD
Query on ZLD

Download CCD File 
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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2, N, T, Y, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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0, 2, 9, A, B, F, H, Q, R, S, Z
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
ACE
Query on ACE

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4
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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0, 2, A, B, I, J, K, L, M, N, Q, X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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0, 1, 9, A, B, J, S, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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0, 9, B, C, I, K, L, P, Q, R
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 

  • 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