6DDG

Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.

Belousoff, M.J.Venugopal, H.Wright, A.Seoner, S.Stuart, I.Stubenrauch, C.Bamert, R.S.Lupton, D.W.Lithgow, T.

(2019) ChemMedChem 14: 527-531

  • DOI: 10.1002/cmdc.201900042
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While the ribosome is a common target for antibiotics, challenges with crystallography can impede the development of new bioactives using structure-based drug design approaches. In this study we exploit common structural features present in linezolid ...

    While the ribosome is a common target for antibiotics, challenges with crystallography can impede the development of new bioactives using structure-based drug design approaches. In this study we exploit common structural features present in linezolid-resistant forms of both methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) to redesign the antibiotic. Enabled by rapid and facile cryoEM structures, this process has identified (S)-2,2-dichloro-N-((3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide (LZD-5) and (S)-2-chloro-N-((3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl) acetamide (LZD-6), which inhibit the ribosomal function and growth of linezolid-resistant MRSA and VRE. The strategy discussed highlights the potential for cryoEM to facilitate the development of novel bioactive materials.


    Organizational Affiliation

    Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia.,Ramaciotti Centre for Electron Microscopy, Monash University, Clayton, 3800, Australia.,School of Chemistry, Monash University, Clayton, 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
A
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplS
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ42
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
276Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P60430
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
C
118Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
D
102Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXS8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
E
116Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW11
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
F
91Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW08
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
G
105Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW17
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
H
217Staphylococcus aureus (strain USA300)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q2FJE0 (Staphylococcus aureus (strain USA300))
Go to UniProtKB:  Q2FJE0
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
I
85Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXT0
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
J
62Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ60
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
K
69Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW14
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
L
217Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW06
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
M
59Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0G2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
N
57Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmF
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZF1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
O
49Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmG2
Find proteins for Q2FY22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FY22
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
P
45Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmH
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FUQ0
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
Q
65Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXQ0
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
R
37Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW29
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
S
207Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW07
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
V
145Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW38
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
W
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW16
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
X
146Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplO
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0A0F8
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Y
144Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW13
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
Z
122Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW33
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
a
119Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FW22
Entity ID: 26
MoleculeChainsLengthOrganism
23S rRNA12923Staphylococcus aureus
Entity ID: 27
MoleculeChainsLengthOrganism
5S rRNA2115Staphylococcus aureus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6M
Query on G6M

Download SDF File 
Download CCD File 
1
2-chloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide
oxazolidinone antibiotic LZD-6
C16 H19 Cl F N3 O4
BLEAWUVPPDXJFJ-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaProgram Grant 1092262

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Type: Author supporting evidence, Other