8E32

E. coli 50S ribosome bound to compound streptogramin analogs SA1 and SB1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 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

Potential for clicked streptogramin analogs

Takahashi, Y.Pellegrino, J.Lee, D.J.Fraser, J.S.Seiple, I.B.

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
Find proteins for P60422 (Escherichia coli (strain K12))
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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
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
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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
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22H [auth P]110Escherichia coliMutation(s): 0 
Gene Names: rplVeryBb3315JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32I [auth Q]56Escherichia coliMutation(s): 0 
Gene Names: rpmFECDEC2D_1303
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34J [auth R]46Escherichia coliMutation(s): 0 
Gene Names: rpmH
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDF (Subject of Investigation/LOI)
Query on UDF

Download Ideal Coordinates CCD File 
L [auth I]~{N}-[(3~{S},6~{S},12~{R},15~{S},16~{R},19~{S},22~{S},24~{R})-12-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethyl]-4,16-dimethyl-24-oxidanyl-2,5,11,14,18,21-hexakis(oxidanylidene)-19-phenyl-3-(phenylmethyl)-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide
C43 H51 N10 O10
GGUGHAXGYRHUOM-RILDDUCRSA-N
UCX (Subject of Investigation/LOI)
Query on UCX

Download Ideal Coordinates CCD File 
K [auth I](3R,4R,5E,10E,12E,14S,16R,23S,26aR)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-yn-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione
C30 H38 F N3 O6
ZFRIDGLVADEYAZ-CLECSTCYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 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