8E45

E. coli 50S ribosome bound to antibiotic analog SLC17


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 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

SLC collection of antibiotic analogs

Yeon, S.K.Pellegrino, J.Lee, D.J.Seiple, I.B.Fraser, J.S.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth K]271Escherichia coliMutation(s): 0 
Gene Names: rplBb3317JW3279
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15D [auth L]144Escherichia coliMutation(s): 0 
Gene Names: rplO
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth M]201Escherichia coliMutation(s): 0 
Gene Names: rplDECMG_02584
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3F [auth N]209Escherichia coliMutation(s): 0 
Gene Names: rplCb3320JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth O]142Escherichia coliMutation(s): 0 
Gene Names: rplMA1UI_03510
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22H [auth P]110Escherichia coliMutation(s): 0 
Gene Names: rplVeryBb3315JW3277
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32I [auth Q]56Escherichia coliMutation(s): 0 
Gene Names: rpmFECDEC2D_1303
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34J [auth R]46Escherichia coliMutation(s): 0 
Gene Names: rpmH
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth I]2,904Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth J]118Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UI6 (Subject of Investigation/LOI)
Query on UI6

Download Ideal Coordinates CCD File 
K [auth I]2-{[(2S,3R,4S,6R)-2-{[(2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-13-{[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy}-3,5,6,8,10,12,14-heptamethyl-15-oxo-1-oxa-6-azacyclopentadecan-11-yl]oxy}-3-hydroxy-6-methyloxan-4-yl](methyl)amino}-N-{[(5S)-3-{(4M)-3-fluoro-4-[(6P)-6-(2-methyl-2H-tetrazol-5-yl)pyridin-3-yl]phenyl}-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide (non-preferred name)
C56 H86 F N9 O15
CCCPNDPSMZJBSW-DALIEQGVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM123159
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128656

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection